Characteristics of Helical Flow through Neck Cutoffs

NASA Astrophysics Data System (ADS)

Richards, D.; Konsoer, K. M.; Turnipseed, C.; Willson, C. S.

2017-12-01

Meander cutoffs and oxbows lakes are a ubiquitous feature of riverine landscapes yet there is a paucity of detailed investigations concentrated on the three-dimensional flow structure through evolving neck cutoffs. The purpose of this research is to investigate and characterize helical flow through neck cutoffs with two different planform configurations: elongate meander loops and serpentine loops. Three-dimensional velocity measurements was collected with an acoustic Doppler current profiler for five cutoffs on the White River, Arkansas. Pronounced helical flow was found through all elongate loop cutoff sites, formed from the balance between centrifugal force resulting from the curving of flow through the cutoff channel and pressure gradient force resulting from water surface super-elevation between primary flow and flow at the entrance and exit of the abandoned loop. The sense of motion of the helical flow caused near-surface fluid to travel outward toward the abandoned loop while near-bed fluid was redirected toward the downstream channel. Another characteristic of the helical flow structure for elongate loop cutoffs was the reversal of helical flow over a relatively short distance, causing patterns of secondary circulation that differed from typical patterns observed through curved channels with point bars. Lastly, helical flow was revealed within zones of strong flow recirculation, enhanced by an exchange of streamwise momentum between shear layers.

Superposition and detection of two helical beams for optical orbital angular momentum communication

NASA Astrophysics Data System (ADS)

Liu, Yi-Dong; Gao, Chunqing; Gao, Mingwei; Qi, Xiaoqing; Weber, Horst

2008-07-01

A loop-like system with a Dove prism is used to generate a collinear superposition of two helical beams with different azimuthal quantum numbers in this manuscript. After the generation of the helical beams distributed on the circle centered at the optical axis by using a binary amplitude grating, the diffractive field is separated into two polarized ones with the same distribution. Rotated by the Dove prism in the loop-like system in counter directions and combined together, the two fields will generate the collinear superposition of two helical beams in certain direction. The experiment shows consistency with the theoretical analysis. This method has potential applications in optical communication by using orbital angular momentum of laser beams (optical vortices).

Renormalization of QCD in the interpolating momentum subtraction scheme at three loops

NASA Astrophysics Data System (ADS)

Gracey, J. A.; Simms, R. M.

2018-04-01

We introduce a more general set of kinematic renormalization schemes than the original momentum subtraction schemes of Celmaster and Gonsalves. These new schemes will depend on a parameter ω , which tags the external momentum of one of the legs of the three-point vertex functions in QCD. In each of the three new schemes, we renormalize QCD in the Landau and maximal Abelian gauges and establish the three-loop renormalization group functions in each gauge. For an application, we evaluate two critical exponents at the Banks-Zaks fixed point and demonstrate that their values appear to be numerically scheme independent in a subrange of the conformal window.

Renormalization scheme dependence of high-order perturbative QCD predictions

NASA Astrophysics Data System (ADS)

Ma, Yang; Wu, Xing-Gang

2018-02-01

Conventionally, one adopts typical momentum flow of a physical observable as the renormalization scale for its perturbative QCD (pQCD) approximant. This simple treatment leads to renormalization scheme-and-scale ambiguities due to the renormalization scheme and scale dependence of the strong coupling and the perturbative coefficients do not exactly cancel at any fixed order. It is believed that those ambiguities will be softened by including more higher-order terms. In the paper, to show how the renormalization scheme dependence changes when more loop terms have been included, we discuss the sensitivity of pQCD prediction on the scheme parameters by using the scheme-dependent {βm ≥2}-terms. We adopt two four-loop examples, e+e-→hadrons and τ decays into hadrons, for detailed analysis. Our results show that under the conventional scale setting, by including more-and-more loop terms, the scheme dependence of the pQCD prediction cannot be reduced as efficiently as that of the scale dependence. Thus a proper scale-setting approach should be important to reduce the scheme dependence. We observe that the principle of minimum sensitivity could be such a scale-setting approach, which provides a practical way to achieve optimal scheme and scale by requiring the pQCD approximate be independent to the "unphysical" theoretical conventions.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chakrabarti, D.; Qiu, J.; Thorn, C. B.

This is the second of a pair of articles on scattering of glue by glue,in which we give the light-cone gauge calculation of the one-loop on-shellhelicity conserving scattering amplitudes for gluon-gluon scattering (neglectingquark loops). The 1/p{sup +} factors in the gluon propagatorare regulated by replacing p{sup +} integrals with discretized sums omitting the p{sup +}=0 terms in each sum. We alsoemploy a novel ultraviolet regulator that is convenient for the light-coneworldsheet description of planar Feynman diagrams. The helicity conservingscattering amplitudes are divergent in the infrared. The infrared divergencesin the elastic one-loop amplitude are shown to cancel, in their contributionto crossmore » sections, against ones in the cross section for unseen bremsstrahlunggluons. We include here the explicit calculation of the latter, because itassumes an unfamiliar form due to the peculiar way discretization of p{sup +} regulates infrared divergences. In resolving the infrareddivergences we employ a covariant definition of jets, which allows a transparentdemonstration of the Lorentz invariance of our final results. Because we usean explicit cutoff of the ultraviolet divergences in exactly four spacetimedimensions, we must introduce explicit counterterms to achieve this finalcovariant result. These counterterms are polynomials in the external momentaof the precise order dictated by power counting. We discuss the modificationsthey entail for the light-cone worldsheet action that reproduces the bareplanar diagrams of the gluonic sector of QCD. The simplest way to do thisis to interpret the QCD string as moving in six spacetime dimensions.« less

On the two-loop virtual QCD corrections to Higgs boson pair production in the standard model

DOE PAGES

Degrassi, Giuseppe; Giardino, Pier Paolo; Gröber, Ramona

2016-07-21

Here, we compute the next-to-leading order virtual QCD corrections to Higgs-pair production via gluon fusion. We also present analytic results for the two-loop contributions to the spin-0 and spin-2 form factors in the amplitude. The reducible contributions, given by the double-triangle diagrams, are evaluated exactly while the two-loop irreducible diagrams are evaluated by an asymptotic expansion in heavy top-quark mass up to and including terms of O(1/mmore » $$8\\atop{t}$$). We estimate that mass effects can reduce the hadronic cross section by at most 10 %, assuming that the finite top-quark mass effects are of similar size in the entire range of partonic energies.« less

Dimensional Transmutation by Monopole Condensation in QCD

NASA Astrophysics Data System (ADS)

Cho, Y. M.

2015-01-01

The dimensional transmutation by the monopole condensation in QCD is reviewed. Using Abelian projection of the gauge potential which projects out the monopole potential gauge independently, we we show that there are two types of gluons: the color neutral binding gluons which plays the role of the confining agent and the colored valence gluons which become confined prisoners. With this we calculate the one-loop QCD effective potential and show the monopole condensation becomes the true vacuum of QCD. We propose to test the existence of two types of gluons experimentally by re-analyzing the existing gluon jets data.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Caola, Fabrizio; Melnikov, Kirill; Rontsch, Raoul

We compute the next-to-leading-order QCD corrections to the production of two Z-bosons in the annihilation of two gluons at the LHC. Being enhanced by a large gluon flux, these corrections provide a distinct and, potentially, the dominant part of the N 3LO QCD contributions to Z-pair production in proton collisions. The gg → ZZ annihilation is a loop-induced process that receives the dominant contribution from loops of five light quarks, that are included in our computation in the massless approximation. We find that QCD corrections increase the gg → ZZ production cross section by O(50%–100%) depending on the values ofmore » the renormalization and factorization scales used in the leading-order computation and the collider energy. Furthermore, the large corrections to the gg → ZZ channel increase the pp → ZZ cross section by about 6% to 8%, exceeding the estimated theoretical uncertainty of the recent next-to-next-to-leading-order QCD calculation.« less

Intracellular segment between transmembrane helices S0 and S1 of BK channel α subunit contains two amphipathic helices connected by a flexible loop

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, Pan; High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui, 230031; Li, Dong

2013-08-02

Highlights: •The loop between S0 and S1 of BK channel was overexpressed and purified in DPC. •NMR studies indicated BK-IS1 contained two helices connected by a flexible loop. •Mg{sup 2+} titration of BK-IS1 indicated two possible binding sites of divalent ions. -- Abstract: The BK channel, a tetrameric potassium channel with very high conductance, has a central role in numerous physiological functions. The BK channel can be activated by intracellular Ca{sup 2+} and Mg{sup 2+}, as well as by membrane depolarization. Unlike other tetrameric potassium channels, the BK channel has seven transmembrane helices (S0–S6) including an extra helix S0. Themore » intracellular segment between S0 and S1 (BK-IS1) is essential to BK channel functions and Asp99 in BK-IS1 is reported to be responsible for Mg{sup 2+} coordination. In this study, BK-IS1 (44–113) was over-expressed using a bacterial system and purified in the presence of detergent micelles for multidimensional heteronuclear nuclear magnetic resonance (NMR) structural studies. Backbone resonance assignment and secondary structure analysis showed that BK-IS1 contains two amphipathic helices connected by a 36-residue loop. Amide {sup 1}H–{sup 15}N heteronuclear NOE analysis indicated that the loop is very flexible, while the two amphipathic helices are possibly stabilized through interaction with the membrane. A solution NMR-based titration assay of BK-IS1 was performed with various concentrations of Mg{sup 2+}. Two residues (Thr45 and Leu46) with chemical shift changes were observed but no, or very minor, chemical shift difference was observed for Asp99, indicating a possible site for binding divalent ions or other modulation partners.« less

Perturbative study of the QCD phase diagram for heavy quarks at nonzero chemical potential: Two-loop corrections

NASA Astrophysics Data System (ADS)

Maelger, J.; Reinosa, U.; Serreau, J.

2018-04-01

We extend a previous investigation [U. Reinosa et al., Phys. Rev. D 92, 025021 (2015), 10.1103/PhysRevD.92.025021] of the QCD phase diagram with heavy quarks in the context of background field methods by including the two-loop corrections to the background field effective potential. The nonperturbative dynamics in the pure-gauge sector is modeled by a phenomenological gluon mass term in the Landau-DeWitt gauge-fixed action, which results in an improved perturbative expansion. We investigate the phase diagram at nonzero temperature and (real or imaginary) chemical potential. Two-loop corrections yield an improved agreement with lattice data as compared to the leading-order results. We also compare with the results of nonperturbative continuum approaches. We further study the equation of state as well as the thermodynamic stability of the system at two-loop order. Finally, using simple thermodynamic arguments, we show that the behavior of the Polyakov loops as functions of the chemical potential complies with their interpretation in terms of quark and antiquark free energies.

Nucleon structure from 2+1-flavor domain-wall QCD

NASA Astrophysics Data System (ADS)

Ohta, Shigemi

2018-03-01

Nucleon-structure calculations of isovector vector-and axialvector-current form factors, transversity and scalar charge, and quark momentum and helicity fractions are reported from two recent 2+1-flavor dynamical domain-wall fermions lattice-QCD ensembles generated jointly by the RIKEN-BNL-Columbia and UKQCD Collaborations with Iwasaki × dislocation-suppressing-determinatn-ratio gauge action at inverse lattice spacing of 1.378(7) GeV and pion mass values of 249.4(3) and 172.3(3) MeV.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deur, Alexandre; Brodsky, Stanley J.; de Téramond, Guy F.

Here, the recent determination of themore » $$\\beta$$--function of the QCD running coupling $$\\alpha_{\\overline{MS}}(Q^2)$$ to five-loops, provides a verification of the convergence of a novel method for determining the fundamental QCD parameter $$\\Lambda_s$$ based on the Light-Front Holographic approach to nonperturbative QCD. The new 5-loop analysis, together with improvements in determining the holographic QCD nonperturbative scale parameter $$\\kappa$$ from hadronic spectroscopy, leads to an improved precision of the value of $$\\Lambda_s$$ in the $${\\overline{MS}}$$ scheme close to a factor of two; we find $$\\Lambda^{(3)}_{\\overline{MS}}=0.339\\pm0.019$$ GeV for $$n_{f}=3$$, in excellent agreement with the world average, $$\\Lambda_{\\overline{MS}}^{(3)}=0.332\\pm0.017$$ GeV. Lastly, we also discuss the constraints imposed on the scale dependence of the strong coupling in the nonperturbative domain by superconformal quantum mechanics and its holographic embedding in anti-de Sitter space.« less

Two loop QCD vertices at the symmetric point

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gracey, J. A.

2011-10-15

We compute the triple gluon, quark-gluon and ghost-gluon vertices of QCD at the symmetric subtraction point at two loops in the MS scheme. In addition we renormalize each of the three vertices in their respective momentum subtraction schemes, MOMggg, MOMq and MOMh. The conversion functions of all the wave functions, coupling constant and gauge parameter renormalization constants of each of the schemes relative to MS are determined analytically. These are then used to derive the three loop anomalous dimensions of the gluon, quark, Faddeev-Popov ghost and gauge parameter as well as the {beta} function in an arbitrary linear covariant gaugemore » for each MOM scheme. There is good agreement of the latter with earlier Landau gauge numerical estimates of Chetyrkin and Seidensticker.« less

Study of the Z{sub 3} symmetry in QCD at finite temperature and chemical potential using a worm algorithm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krein, Gastao; Leme, Rafael R.; Woitek, Marcio

Traditional Monte Carlo simulations of QCD in the presence of a baryon chemical potential are plagued by the complex phase problem and new numerical approaches are necessary for studying the phase diagram of the theory. In this work we consider a Z{sub 3} Polyakov loop model for the deconfining phase transition in QCD and discuss how a flux representation of the model in terms of dimer and monomer variable solves the complex action problem. We present results of numerical simulations using a worm algorithm for the specific heat and two-point correlation function of Polyakov loops. Evidences of a first ordermore » deconfinement phase transition are discussed.« less

Wilson loops and QCD/string scattering amplitudes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Makeenko, Yuri; Olesen, Poul; Niels Bohr International Academy, Niels Bohr Institute, Blegdamsvej 17, 2100 Copenhagen O

2009-07-15

We generalize modern ideas about the duality between Wilson loops and scattering amplitudes in N=4 super Yang-Mills theory to large N QCD by deriving a general relation between QCD meson scattering amplitudes and Wilson loops. We then investigate properties of the open-string disk amplitude integrated over reparametrizations. When the Wilson-loop is approximated by the area behavior, we find that the QCD scattering amplitude is a convolution of the standard Koba-Nielsen integrand and a kernel. As usual poles originate from the first factor, whereas no (momentum-dependent) poles can arise from the kernel. We show that the kernel becomes a constant whenmore » the number of external particles becomes large. The usual Veneziano amplitude then emerges in the kinematical regime, where the Wilson loop can be reliably approximated by the area behavior. In this case, we obtain a direct duality between Wilson loops and scattering amplitudes when spatial variables and momenta are interchanged, in analogy with the N=4 super Yang-Mills theory case.« less

The Role of Magnetic Helicity in Structuring the Solar Corona

NASA Technical Reports Server (NTRS)

Knizhnik, K. J.; Antiochos, S. K.; DeVore, C. R.

2017-01-01

Two of the most widely observed and striking features of the Suns magnetic field are coronal loops, which are smooth and laminar, and prominences or filaments, which are strongly sheared. Loops are puzzling because they show little evidence of tangling or braiding, at least on the quiet Sun, despite the chaotic nature of the solar surface convection. Prominences are mysterious because the origin of their underlying magnetic structure filament channels is poorly understood at best. These two types of features would seem to be quite unrelated and wholly distinct. We argue that, on the contrary, they are inextricably linked and result from a single process: the injection of magnetic helicity into the corona by photospheric motions and the subsequent evolution of this helicity by coronal reconnection. In this paper, we present numerical simulations of the response of a Parker (1972) corona to photospheric driving motions that have varying degrees of helicity preference. We obtain four main conclusions: (1) in agreement with the helicity condensation model of Antiochos (2013), the inverse cascade of helicity by magnetic reconnection in the corona results in the formation of filament channels localized about polarity inversion lines; (2) this same process removes most complex fine structure from the rest of the corona, resulting in smooth and laminar coronal loops; (3) the amount of remnant tangling in coronal loops is inversely dependent on the net helicity injected by the driving motions; and (4) the structure of the solar corona depends only on the helicity preference of the driving motions and not on their detailed time dependence. We discuss the implications of our results for high-resolution observations of the corona.

THE ROLE OF MAGNETIC HELICITY IN STRUCTURING THE SOLAR CORONA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Knizhnik, K. J.; Antiochos, S. K.; DeVore, C. R.

Two of the most widely observed and striking features of the Sun's magnetic field are coronal loops, which are smooth and laminar, and prominences or filaments, which are strongly sheared. Loops are puzzling because they show little evidence of tangling or braiding, at least on the quiet Sun, despite the chaotic nature of the solar surface convection. Prominences are mysterious because the origin of their underlying magnetic structure—filament channels—is poorly understood at best. These two types of features would seem to be quite unrelated and wholly distinct. We argue that, on the contrary, they are inextricably linked and result frommore » a single process: the injection of magnetic helicity into the corona by photospheric motions and the subsequent evolution of this helicity by coronal reconnection. In this paper, we present numerical simulations of the response of a Parker (1972) corona to photospheric driving motions that have varying degrees of helicity preference. We obtain four main conclusions: (1) in agreement with the helicity condensation model of Antiochos (2013), the inverse cascade of helicity by magnetic reconnection in the corona results in the formation of filament channels localized about polarity inversion lines; (2) this same process removes most complex fine structure from the rest of the corona, resulting in smooth and laminar coronal loops; (3) the amount of remnant tangling in coronal loops is inversely dependent on the net helicity injected by the driving motions; and (4) the structure of the solar corona depends only on the helicity preference of the driving motions and not on their detailed time dependence. We discuss the implications of our results for high-resolution observations of the corona.« less

Hard-thermal-loop perturbation theory to two loops

NASA Astrophysics Data System (ADS)

Andersen, Jens O.; Braaten, Eric; Petitgirard, Emmanuel; Strickland, Michael

2002-10-01

We calculate the pressure for pure-glue QCD at high temperature to two-loop order using hard-thermal-loop (HTL) perturbation theory. At this order, all the ultraviolet divergences can be absorbed into renormalizations of the vacuum energy density and the HTL mass parameter. We determine the HTL mass parameter by a variational prescription. The resulting predictions for the pressure fail to agree with results from lattice gauge theory at temperatures for which they are available.

Two-loop hard-thermal-loop thermodynamics with quarks

NASA Astrophysics Data System (ADS)

Andersen, Jens O.; Petitgirard, Emmanuel; Strickland, Michael

2004-08-01

We calculate the quark contribution to the free energy of a hot quark-gluon plasma to two-loop order using hard-thermal-loop (HTL) perturbation theory. All ultraviolet divergences can be absorbed into renormalizations of the vacuum energy and the HTL quark and gluon mass parameters. The quark and gluon HTL mass parameters are determined self-consistently by a variational prescription. Combining the quark contribution with the two-loop HTL perturbation theory free energy for pure glue we obtain the total two-loop QCD free energy. Comparisons are made with lattice estimates of the free energy for Nf=2 and with exact numerical results obtained in the large-Nf limit.

Heavy quark form factors at two loops

NASA Astrophysics Data System (ADS)

Ablinger, J.; Behring, A.; Blümlein, J.; Falcioni, G.; De Freitas, A.; Marquard, P.; Rana, N.; Schneider, C.

2018-05-01

We compute the two-loop QCD corrections to the heavy quark form factors in the case of the vector, axial-vector, scalar and pseudoscalar currents up to second order in the dimensional parameter ɛ =(4 -D )/2 . These terms are required in the renormalization of the higher-order corrections to these form factors.

Higgs bosons with large transverse momentum at the LHC

NASA Astrophysics Data System (ADS)

Kudashkin, Kirill; Lindert, Jonas M.; Melnikov, Kirill; Wever, Christopher

2018-07-01

We compute the next-to-leading order QCD corrections to the production of Higgs bosons with large transverse momentum p⊥ ≫ 2mt at the LHC. To accomplish this, we combine the two-loop amplitudes for processes gg → Hg, qg → Hq and q q bar → Hg, recently computed in the approximation of nearly massless top quarks, with the numerical calculation of the squared one-loop amplitudes for gg → Hgg, qg → Hqg and q q bar → Hgg processes. The latter computation is performed with OpenLoops. We find that the QCD corrections to the Higgs transverse momentum distribution at very high p⊥ are large but quite similar to the QCD corrections obtained for point-like Hgg coupling. Our result removes one of the largest sources of theoretical uncertainty in the description of high-p⊥ Higgs boson production and opens a way to use the high-p⊥ region to search for physics beyond the Standard Model.

Next-to-Leading-Order QCD Corrections to Higgs Boson Plus Jet Production with Full Top-Quark Mass Dependence

NASA Astrophysics Data System (ADS)

Jones, S. P.; Kerner, M.; Luisoni, G.

2018-04-01

We present the next-to-leading-order QCD corrections to the production of a Higgs boson in association with one jet at the LHC including the full top-quark mass dependence. The mass of the bottom quark is neglected. The two-loop integrals appearing in the virtual contribution are calculated numerically using the method of sector decomposition. We study the Higgs boson transverse momentum distribution, focusing on the high pt ,H region, where the top-quark loop is resolved. We find that the next-to-leading-order QCD corrections are large but that the ratio of the next-to-leading-order to leading-order result is similar to that obtained by computing in the limit of large top-quark mass.

Next-to-Leading-Order QCD Corrections to Higgs Boson Plus Jet Production with Full Top-Quark Mass Dependence.

PubMed

Jones, S P; Kerner, M; Luisoni, G

2018-04-20

We present the next-to-leading-order QCD corrections to the production of a Higgs boson in association with one jet at the LHC including the full top-quark mass dependence. The mass of the bottom quark is neglected. The two-loop integrals appearing in the virtual contribution are calculated numerically using the method of sector decomposition. We study the Higgs boson transverse momentum distribution, focusing on the high p_{t,H} region, where the top-quark loop is resolved. We find that the next-to-leading-order QCD corrections are large but that the ratio of the next-to-leading-order to leading-order result is similar to that obtained by computing in the limit of large top-quark mass.

Flavor-singlet baryons in the graded symmetry approach to partially quenched QCD

NASA Astrophysics Data System (ADS)

Hall, Jonathan M. M.; Leinweber, Derek B.

2016-11-01

Progress in the calculation of the electromagnetic properties of baryon excitations in lattice QCD presents new challenges in the determination of sea-quark loop contributions to matrix elements. A reliable estimation of the sea-quark loop contributions represents a pressing issue in the accurate comparison of lattice QCD results with experiment. In this article, an extension of the graded symmetry approach to partially quenched QCD is presented, which builds on previous theory by explicitly including flavor-singlet baryons in its construction. The formalism takes into account the interactions among both octet and singlet baryons, octet mesons, and their ghost counterparts; the latter enables the isolation of the quark-flow disconnected sea-quark loop contributions. The introduction of flavor-singlet states enables systematic studies of the internal structure of Λ -baryon excitations in lattice QCD, including the topical Λ (1405 ).

Three-loop hard-thermal-loop perturbation theory thermodynamics at finite temperature and finite baryonic and isospin chemical potential

NASA Astrophysics Data System (ADS)

Andersen, Jens O.; Haque, Najmul; Mustafa, Munshi G.; Strickland, Michael

2016-03-01

In a previous paper [N. Haque et al., J. High Energy Phys. 05 (2014) 27], we calculated the three-loop thermodynamic potential of QCD at finite temperature T and quark chemical potentials μq using the hard-thermal-loop perturbation theory (HTLpt) reorganization of finite temperature and density QCD. The result allows us to study the thermodynamics of QCD at finite temperature and finite baryon, strangeness, and isospin chemical potentials μB, μS, and μI. We calculate the pressure at nonzero μB and μI with μS=0 , and the energy density, the entropy density, the trace anomaly, and the speed of sound at nonzero μI with μB=μS=0 . The second- and fourth-order isospin susceptibilities are calculated at μB=μS=μI=0 . Our results can be directly compared to lattice QCD without Taylor expansions around μq=0 since QCD has no sign problem at μB=μS=0 and finite isospin chemical potential μI.

Renormalization scheme dependence of the two-loop QCD corrections to the neutral Higgs-boson masses in the MSSM.

PubMed

Borowka, S; Hahn, T; Heinemeyer, S; Heinrich, G; Hollik, W

Reaching a theoretical accuracy in the prediction of the lightest MSSM Higgs-boson mass, [Formula: see text], at the level of the current experimental precision requires the inclusion of momentum-dependent contributions at the two-loop level. Recently two groups presented the two-loop QCD momentum-dependent corrections to [Formula: see text] (Borowka et al., Eur Phys J C 74(8):2994, 2014; Degrassi et al., Eur Phys J C 75(2):61, 2015), using a hybrid on-shell-[Formula: see text] scheme, with apparently different results. We show that the differences can be traced back to a different renormalization of the top-quark mass, and that the claim in Ref. Degrassi et al. (Eur Phys J C 75(2):61, 2015) of an inconsistency in Ref. Borowka et al. (Eur Phys J C 74(8):2994, 2014) is incorrect. We furthermore compare consistently the results for [Formula: see text] obtained with the top-quark mass renormalized on-shell and [Formula: see text]. The latter calculation has been added to the FeynHiggs package and can be used to estimate missing higher-order corrections beyond the two-loop level.

Third generation sfermion decays into Z and W gauge bosons: Full one-loop analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arhrib, Abdesslam; LPHEA, Departement de Physique, Faculte des Sciences-Semlalia, B.P. 2390 Marrakech; Benbrik, Rachid

2005-05-01

The complete one-loop radiative corrections to third-generation scalar fermions into gauge bosons Z and W{sup {+-}} is considered. We focus on f-tilde{sub 2}{yields}Zf-tilde{sub 1} and f-tilde{sub i}{yields}W{sup {+-}}f-tilde{sub j}{sup '}, f,f{sup '}=t,b. We include SUSY-QCD, QED, and full electroweak corrections. It is found that the electroweak corrections can be of the same order as the SUSY-QCD corrections. The two sets of corrections interfere destructively in some region of parameter space. The full one-loop correction can reach 10% in some supergravity scenario, while in model independent analysis like general the minimal supersymmetric standard model, the one-loop correction can reach 20% formore » large tan{beta} and large trilinear soft breaking terms A{sub b}.« less

Critical end point in the presence of a chiral chemical potential

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cui, Z. -F.; Cloët, I. C.; Lu, Y.

A class of Polyakov-loop-modified Nambu-Jona-Lasinio models has been used to support a conjecture that numerical simulations of lattice-regularized QCD defined with a chiral chemical potential can provide information about the existence and location of a critical end point in the QCD phase diagram drawn in the plane spanned by baryon chemical potential and temperature. That conjecture is challenged by conflicts between the model results and analyses of the same problem using simulations of lattice-regularized QCD (lQCD) and well-constrained Dyson-Schwinger equation (DSE) studies. We find the conflict is resolved in favor of the lQCD and DSE predictions when both a physicallymore » motivated regularization is employed to suppress the contribution of high-momentum quark modes in the definition of the effective potential connected with the Polyakov-loop-modified Nambu-Jona-Lasinio models and the four-fermion coupling in those models does not react strongly to changes in the mean field that is assumed to mock-up Polyakov-loop dynamics. With the lQCD and DSE predictions thus confirmed, it seems unlikely that simulations of lQCD with mu(5) > 0 can shed any light on a critical end point in the regular QCD phase diagram.« less

Two-loop integrals for CP-even heavy quarkonium production and decays: elliptic sectors

NASA Astrophysics Data System (ADS)

Chen, Long-Bin; Jiang, Jun; Qiao, Cong-Feng

2018-04-01

By employing the differential equations, we compute analytically the elliptic sectors of two-loop master integrals appearing in the NNLO QCD corrections to CP-even heavy quarkonium exclusive production and decays, which turns out to be the last and toughest part in the relevant calculation. The integrals are found can be expressed as Goncharov polylogarithms and iterative integrals over elliptic functions. The master integrals may be applied to some other NNLO QCD calculations about heavy quarkonium exclusive production, like {γ}^{\\ast}γ \\to Q\\overline{Q} , {e}+{e}-\\to γ +Q\\overline{Q} , and H/{Z}^0\\to γ +Q\\overline{Q} , heavy quarkonium exclusive decays, and also the CP-even heavy quarkonium inclusive production and decays.

The massive soft anomalous dimension matrix at two loops

NASA Astrophysics Data System (ADS)

Mitov, Alexander; Sterman, George; Sung, Ilmo

2009-05-01

We study two-loop anomalous dimension matrices in QCD and related gauge theories for products of Wilson lines coupled at a point. We verify by an analysis in Euclidean space that the contributions to these matrices from diagrams that link three massive Wilson lines do not vanish in general. We show, however, that for two-to-two processes the two-loop anomalous dimension matrix is diagonal in the same color-exchange basis as the one-loop matrix for arbitrary masses at absolute threshold and for scattering at 90 degrees in the center of mass. This result is important for applications of threshold resummation in heavy quark production.

Massive QCD Amplitudes at Higher Orders

NASA Astrophysics Data System (ADS)

Moch, S.; Mitov, A.

2007-11-01

We consider the factorisation properties of on-shell QCD amplitudes with massive partons in the limit when all kinematical invariants are large compared to the parton mass and discuss the structure of their infrared singularities. The dimensionally regulated soft poles and the large collinear logarithms of the parton masses exponentiate to all orders. Based on this factorisation a simple relation between massless and massive scattering amplitudes in gauge theories can be established. We present recent applications of this relation for the calculation of the two-loop virtual QCD corrections to the hadro-production of heavy quarks.

Comparative assessment of the efficacy of closed helical loop and T-loop for space closure in lingual orthodontics-a finite element study.

PubMed

Chacko, Ajay; Tikku, Tripti; Khanna, Rohit; Maurya, Rana Pratap; Srivastava, Kamna

2018-05-28

Retraction in lingual orthodontics has biomechanical differences when compared to labial orthodontics, which is not yet established. Thus, we have intended to compare the biomechanical characteristics of closed helical loop and T-loop on 1 mm activation with 30° of compensatory curvatures during retraction in lingual orthodontics. STb lingual brackets were indirectly bonded to maxillary typhodont model that was scanned to obtain FEM model. Closed helical loop (2 × 7 mm) and T-loop (6 × 2 × 7 mm) of 0.016″ × 0.016″ TMA wire were modeled without preactivation bends. Preactivation bends at 30° were given in the software. Boundary conditions were set. The force (F) and moment (M) of both the loops were determined on 1 mm activation, using ANSYS software. M/F ratio was also calculated for both the loops. T-loop exerted less force, thus increased M/F ratio as compared to closed helical loop on 1 mm activation. When torque has to be preserved in the anterior segment during retraction in lingual orthodontics, T-loop can be preferred over closed helical loop.

Numerical Simulations of Helicity Condensation in the Solar Corona

NASA Technical Reports Server (NTRS)

Zhao, L.; DeVore, C. R.; Antiochos, S. K.; Zurbuchen, T. H.

2015-01-01

The helicity condensation model has been proposed by Antiochos (2013) to explain the observed smoothness of coronal loops and the observed buildup of magnetic shear at filament channels. The basic hypothesis of the model is that magnetic reconnection in the corona causes the magnetic stress injected by photospheric motions to collect only at those special locations where prominences form. In this work we present the first detailed quantitative MHD simulations of the reconnection evolution proposed by the helicity condensation model. We use the well-known ansatz of modeling the closed corona as an initially uniform field between two horizontal photospheric plates. The system is driven by applying photospheric rotational flows that inject magnetic helicity into the system. The flows are confined to a finite region on the photosphere so as to mimic the finite flux system of, for example, a bipolar active region. The calculations demonstrate that, contrary to common belief, coronal loops having opposite helicity do not reconnect, whereas loops having the same sense of helicity do reconnect. Furthermore, we find that for a given amount of helicity injected into the corona, the evolution of the magnetic shear is insensitive to whether the pattern of driving photospheric motions is fixed or quasi-random. In all cases, the shear propagates via reconnection to the boundary of the flow region while the total magnetic helicity is conserved, as predicted by the model. We discuss the implications of our results for solar observations and for future, more realistic simulations of the helicity condensation process.

NNLO splitting and coefficient functions with time-like kinematics

NASA Astrophysics Data System (ADS)

Mitov, A.; Moch, S.; Vogt, A.

2006-10-01

We discuss recent results on the three-loop (next-to-next-to-leading order, NNLO) time-like splitting functions of QCD and the two-loop (NNLO) coefficient functions in one-particle inclusive e+e--annihilation. These results form the basis for extracting fragmentation functions for light and heavy flavors with NNLO accuracy that will be needed at the LHC and ILC. The two-loop calculations have been performed in Mellin space based on a new method, the main features of which we also describe briefly.

Cardiac looping may be driven by compressive loads resulting from unequal growth of the heart and pericardial cavity. Observations on a physical simulation model

PubMed Central

Bayraktar, Meriç; Männer, Jörg

2014-01-01

The transformation of the straight embryonic heart tube into a helically wound loop is named cardiac looping. Such looping is regarded as an essential process in cardiac morphogenesis since it brings the building blocks of the developing heart into an approximation of their definitive topographical relationships. During the past two decades, a large number of genes have been identified which play important roles in cardiac looping. However, how genetic information is physically translated into the dynamic form changes of the looping heart is still poorly understood. The oldest hypothesis of cardiac looping mechanics attributes the form changes of the heart loop (ventral bending → simple helical coiling → complex helical coiling) to compressive loads resulting from growth differences between the heart and the pericardial cavity. In the present study, we have tested the physical plausibility of this hypothesis, which we call the growth-induced buckling hypothesis, for the first time. Using a physical simulation model, we show that growth-induced buckling of a straight elastic rod within the confined space of a hemispherical cavity can generate the same sequence of form changes as observed in the looping embryonic heart. Our simulation experiments have furthermore shown that, under bilaterally symmetric conditions, growth-induced buckling generates left- and right-handed helices (D-/L-loops) in a 1:1 ratio, while even subtle left- or rightward displacements of the caudal end of the elastic rod at the pre-buckling state are sufficient to direct the buckling process toward the generation of only D- or L-loops, respectively. Our data are discussed with respect to observations made in biological “models.” We conclude that compressive loads resulting from unequal growth of the heart and pericardial cavity play important roles in cardiac looping. Asymmetric positioning of the venous heart pole may direct these forces toward a biased generation of D- or L-loops. PMID:24772086

Transverse spin structure of the nucleon from lattice-QCD simulations.

PubMed

Göckeler, M; Hägler, Ph; Horsley, R; Nakamura, Y; Pleiter, D; Rakow, P E L; Schäfer, A; Schierholz, G; Stüben, H; Zanotti, J M

2007-06-01

We present the first calculation in lattice QCD of the lowest two moments of transverse spin densities of quarks in the nucleon. They encode correlations between quark spin and orbital angular momentum. Our dynamical simulations are based on two flavors of clover-improved Wilson fermions and Wilson gluons. We find significant contributions from certain quark helicity flip generalized parton distributions, leading to strongly distorted densities of transversely polarized quarks in the nucleon. In particular, based on our results and recent arguments by Burkardt [Phys. Rev. D 72, 094020 (2005)], we predict that the Boer-Mulders function h(1/1), describing correlations of transverse quark spin and intrinsic transverse momentum of quarks, is large and negative for both up and down quarks.

Small-x asymptotics of the gluon helicity distribution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kovchegov, Yuri V.; Pitonyak, Daniel; Sievert, Matthew D.

2017-10-27

Here, we determine the small-x asymptotics of the gluon helicity distribution in a proton at leading order in perturbative QCD at large N c. To achieve this, we begin by evaluating the dipole gluon helicity TMD at small x. In the process we obtain an interesting new result: in contrast to the unpolarized dipole gluon TMD case, the operator governing the small-x behavior of the dipole gluon helicity TMD is different from the operator corresponding to the polarized dipole scattering amplitude (used in our previous work to determine the small-x asymptotics of the quark helicity distribution).

Mrst '96: Current Ideas in Theoretical Physics - Proceedings of the Eighteenth Annual Montréal-Rochester-Syracuse-Toronto Meeting

NASA Astrophysics Data System (ADS)

O'Donnell, Patrick J.; Smith, Brian Hendee

1996-11-01

The Table of Contents for the full book PDF is as follows: * Preface * Roberto Mendel, An Appreciaton * The Infamous Coulomb Gauge * Renormalized Path Integral in Quantum Mechanics * New Analysis of the Divergence of Perturbation Theory * The Last of the Soluble Two Dimensional Field Theories? * Rb and Heavy Quark Mixing * Rb Problem: Loop Contributions and Supersymmetry * QCD Radiative Effects in Inclusive Hadronic B Decays * CP-Violating Dipole Moments of Quarks in the Kobayashi-Maskawa Model * Hints of Dynamical Symmetry Breaking? * Pi Pi Scattering in an Effective Chiral Lagrangian * Pion-Resonance Parameters from QCD Sum Rules * Higgs Theorem, Effective Action, and its Gauge Invariance * SUSY and the Decay H_2^0 to gg * Effective Higgs-to-Light Quark Coupling Induced by Heavy Quark Loops * Heavy Charged Lepton Production in Superstring Inspired E6 Models * The Elastic Properties of a Flat Crystalline Membrane * Gauge Dependence of Topological Observables in Chern-Simons Theory * Entanglement Entropy From Edge States * A Simple General Treatment of Flavor Oscillations * From Schrödinger to Maupertuis: Least Action Principles from Quantum Mechanics * The Matrix Method for Multi-Loop Feynman Integrals * Simplification in QCD and Electroweak Calculations * Programme * List of Participants

The singular behavior of one-loop massive QCD amplitudes with one external soft gluon

NASA Astrophysics Data System (ADS)

Bierenbaum, Isabella; Czakon, Michał; Mitov, Alexander

2012-03-01

We calculate the one-loop correction to the soft-gluon current with massive fermions. This current is process independent and controls the singular behavior of one-loop massive QCD amplitudes in the limit when one external gluon becomes soft. The result derived in this work is the last missing process-independent ingredient needed for numerical evaluation of observables with massive fermions at hadron colliders at the next-to-next-to-leading order.

One-loop QCD thermodynamics in a strong homogeneous and static magnetic field

NASA Astrophysics Data System (ADS)

Rath, Shubhalaxmi; Patra, Binoy Krishna

2017-12-01

We have studied how the equation of state of thermal QCD with two light flavors is modified in a strong magnetic field. We calculate the thermodynamic observables of hot QCD matter up to one-loop, where the magnetic field affects mainly the quark contribution and the gluon part is largely unaffected except for the softening of the screening mass. We have first calculated the pressure of a thermal QCD medium in a strong magnetic field, where the pressure at fixed temperature increases with the magnetic field faster than the increase with the temperature at constant magnetic field. This can be understood from the dominant scale of thermal medium in the strong magnetic field, being the magnetic field, in the same way that the temperature dominates in a thermal medium in the absence of magnetic field. Thus although the presence of a strong magnetic field makes the pressure of hot QCD medium larger, the dependence of pressure on the temperature becomes less steep. Consistent with the above observations, the entropy density is found to decrease with the temperature in the presence of a strong magnetic field which is again consistent with the fact that the strong magnetic field restricts the dynamics of quarks to two dimensions, hence the phase space becomes squeezed resulting in the reduction of number of microstates. Moreover the energy density is seen to decrease and the speed of sound of thermal QCD medium increases in the presence of a strong magnetic field. These findings could have phenomenological implications in heavy ion collisions because the expansion dynamics of the medium produced in non-central ultra-relativistic heavy ion collisions is effectively controlled by both the energy density and the speed of sound.

Effective holographic models for QCD: Glueball spectrum and trace anomaly

NASA Astrophysics Data System (ADS)

Ballon-Bayona, Alfonso; Boschi-Filho, Henrique; Mamani, Luis A. H.; Miranda, Alex S.; Zanchin, Vilson T.

2018-02-01

We investigate effective holographic models for QCD arising from five-dimensional dilaton gravity. The models are characterized by a dilaton with a mass term in the UV, dual to a CFT deformation by a relevant operator, and quadratic in the IR. The UV constraint leads to the explicit breaking of conformal symmetry, whereas the IR constraint guarantees linear confinement. We propose semianalytic interpolations between the UV and the IR and obtain a spectrum for scalar and tensor glueballs consistent with lattice QCD data. We use the glueball spectrum as a physical constraint to find the evolution of the model parameters as the mass term goes to 0. Finally, we reproduce the universal result for the trace anomaly of deformed CFTs and propose a dictionary between this result and the QCD trace anomaly. A nontrivial consequence of this dictionary is the emergence of a β function similar to the two-loop perturbative QCD result.

HIT-SI Injector Voltage Measurements Using Injector Langmuir Probes

NASA Astrophysics Data System (ADS)

Aboul Hosn, Rabih; Smith, Roger; Jarboe, Thomas

2006-10-01

A pair of Langmuir probe arrays have been designed and built to measure floating potentials of the plasma at the injector mouth of the HIT-SI device. The Helicity Injected Torus using Steady Inductive Helicity Injection (HIT-SI) [1,2] is a ``bow tie'' spheromak using an electrodeless formation and sustainment concept. HIT-SI is powered by two inductive helicity injectors operated in quadrature to maintain a constant helicity injection rate. The electric probes consist of an array of four floating potential Langmuir probes measuring the voltage distribution in each injector from the shell to midpoint of the injector mouth. The probe measurements combine to determine the part of the injector loop voltage driving the n = 0 spheromak equilibrium region. Preliminary data suggest the spheromak voltage is the loop voltage minus the nearly constant injector voltage of 150-180 volts. These probe data will be used to calculate the helicity decay time of the spheromak. [1] T. R. Jarboe. Steady inductive helicity injection and its application to a high-beta spheromak. Fusion Technology, 36(1):85--91, July 1999. [2] P.E.Sieck et al., ``Demonstration of Steady Inductive Helicity Injection'', Nuc. Fusion, in press (2006).

Exclusive QCD processes, quark-hadron duality, and the transition to perturbative QCD

NASA Astrophysics Data System (ADS)

Corianò, Claudio; Li, Hsiang-nan; Savkli, Cetin

1998-07-01

Experiments at CEBAF will scan the intermediate-energy region of the QCD dynamics for the nucleon form factors and for Compton Scattering. These experiments will definitely clarify the role of resummed perturbation theory and of quark-hadron duality (QCD sum rules) in this regime. With this perspective in mind, we review the factorization theorem of perturbative QCD for exclusive processes at intermediate energy scales, which embodies the transverse degrees of freedom of a parton and the Sudakov resummation of the corresponding large logarithms. We concentrate on the pion and proton electromagnetic form factors and on pion Compton scattering. New ingredients, such as the evolution of the pion wave function and the complete two-loop expression of the Sudakov factor, are included. The sensitivity of our predictions to the infrared cutoff for the Sudakov evolution is discussed. We also elaborate on QCD sum rule methods for Compton Scattering, which provide an alternative description of this process. We show that, by comparing the local duality analysis to resummed perturbation theory, it is possible to describe the transition of exclusive processes to perturbative QCD.

Form factors and differential branching ratio of B →K μ+μ- in AdS/QCD

NASA Astrophysics Data System (ADS)

Momeni, S.; Khosravi, R.

2018-03-01

The holographic distribution amplitudes (DAs) for the K pseudoscalar meson are derived. For this aim, the light-front wave function (LFWF) of the K meson is extracted within the framework of the anti-de Sitter/quantum chromodynamics (AdS/QCD) correspondence. We consider a momentum-dependent (dynamical) helicity wave function that contains the dynamical spin effects. We use the LFWF to predict the radius and the electromagnetic form factor of the kaon and compare them with the experimental values. Then, the holographic twist-2 DA of K meson ϕK(α ,μ ) is investigated and compared with the result of the light-cone sum rules (LCSR). The transition form factors of the semileptonic B →K ℓ+ℓ- decays are derived from the holographic DAs of the kaon. With the help of these form factors, the differential branching ratio of the B →K μ+μ- on q2 is plotted. A comparison is made between our prediction in AdS/QCD and the results obtained from two models including the LCSR and the lattice QCD as well as the experimental values.

Thermal stability of DNA quadruplex-duplex hybrids.

PubMed

Lim, Kah Wai; Khong, Zi Jian; Phan, Anh Tuân

2014-01-14

DNA has the capacity to adopt several distinct structural forms, such as duplex and quadruplex helices, which have been implicated in cellular processes and shown to exhibit important functional properties. Quadruplex-duplex hybrids, generated from the juxtaposition of these two structural elements, could find applications in therapeutics and nanotechnology. Here we used NMR and CD spectroscopy to investigate the thermal stability of two classes of quadruplex-duplex hybrids comprising fundamentally distinct modes of duplex and quadruplex connectivity: Construct I involves the coaxial orientation of the duplex and quadruplex helices with continual base stacking across the two components; Construct II involves the orthogonal orientation of the duplex and quadruplex helices with no base stacking between the two components. We have found that for both constructs, the stability of the quadruplex generally increases with the length of the stem-loop incorporated, with respect to quadruplexes comprising nonstructured loops of the same length, which showed a continuous drop in stability with increasing loop length. The stability of these complexes, particularly Construct I, can be substantially influenced by the base-pair steps proximal to the quadruplex-duplex junction. Bulges at the junction are largely detrimental to the adoption of the desired G-quadruplex topology for Construct I but not for Construct II. These findings should facilitate future design and prediction of quadruplex-duplex hybrids.

Search for C=+ charmonium and bottomonium states in e{sup +}e{sup -}{yields}{gamma}+ X at B factories

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li Dan; Chao Kuangta; He Zhiguo

2009-12-01

We study the production of C=+ charmonium states X in e{sup +}e{sup -}{yields}{gamma}+X at B factories with X={eta}{sub c}(nS) (n=1, 2, 3), {chi}{sub cJ}(mP) (m=1, 2), and {sup 1}D{sub 2}(1D). In the S- and P-wave case, contributions of QED with one-loop QCD corrections are calculated within the framework of nonrelativistic QCD (NRQCD), and in the D-wave case only the QED contribution is considered. We find that in most cases the one-loop QCD corrections are negative and moderate, in contrast to the case of double charmonium production e{sup +}e{sup -}{yields}J/{psi}+X, where one-loop QCD corrections are positive and large in most cases.more » We also find that the production cross sections of some of these states in e{sup +}e{sup -}{yields}{gamma}+X are larger than that in e{sup +}e{sup -}{yields}J/{psi}+X by an order of magnitude even after the negative one-loop QCD corrections are included. We then argue that search for the X(3872), X(3940), Y(3940), and X(4160) in e{sup +}e{sup -}{yields}{gamma}+X at B factories may be helpful to clarify the nature of these states. For completeness, the production of bottomonium states in e{sup +}e{sup -} annihilation is also discussed.« less

Analytic Result for the Two-loop Six-point NMHV Amplitude in N = 4 Super Yang-Mills Theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dixon, Lance J.; /SLAC; Drummond, James M.

2012-02-15

We provide a simple analytic formula for the two-loop six-point ratio function of planar N = 4 super Yang-Mills theory. This result extends the analytic knowledge of multi-loop six-point amplitudes beyond those with maximal helicity violation. We make a natural ansatz for the symbols of the relevant functions appearing in the two-loop amplitude, and impose various consistency conditions, including symmetry, the absence of spurious poles, the correct collinear behavior, and agreement with the operator product expansion for light-like (super) Wilson loops. This information reduces the ansatz to a small number of relatively simple functions. In order to fix these parametersmore » uniquely, we utilize an explicit representation of the amplitude in terms of loop integrals that can be evaluated analytically in various kinematic limits. The final compact analytic result is expressed in terms of classical polylogarithms, whose arguments are rational functions of the dual conformal cross-ratios, plus precisely two functions that are not of this type. One of the functions, the loop integral {Omega}{sup (2)}, also plays a key role in a new representation of the remainder function R{sub 6}{sup (2)} in the maximally helicity violating sector. Another interesting feature at two loops is the appearance of a new (parity odd) x (parity odd) sector of the amplitude, which is absent at one loop, and which is uniquely determined in a natural way in terms of the more familiar (parity even) x (parity even) part. The second non-polylogarithmic function, the loop integral {tilde {Omega}}{sup (2)}, characterizes this sector. Both {Omega}{sup (2)} and {tilde {Omega}}{sup (2)} can be expressed as one-dimensional integrals over classical polylogarithms with rational arguments.« less

Optical fiber loops and helices: tools for integrated photonic device characterization and microfluidic trapping

NASA Astrophysics Data System (ADS)

Ren, Yundong; Zhang, Rui; Ti, Chaoyang; Liu, Yuxiang

2016-09-01

Tapered optical fibers can deliver guided light into and carry light out of micro/nanoscale systems with low loss and high spatial resolution, which makes them ideal tools in integrated photonics and microfluidics. Special geometries of tapered fibers are desired for probing monolithic devices in plane as well as optical manipulation of micro particles in fluids. However, for many specially shaped tapered fibers, it remains a challenge to fabricate them in a straightforward, controllable, and repeatable way. In this work, we fabricated and characterized two special geometries of tapered optical fibers, namely fiber loops and helices, that could be switched between one and the other. The fiber loops in this work are distinct from previous ones in terms of their superior mechanical stability and high optical quality factors in air, thanks to a post-annealing process. We experimentally measured an intrinsic optical quality factor of 32,500 and a finesse of 137 from a fiber loop. A fiber helix was used to characterize a monolithic cavity optomechanical device. Moreover, a microfluidic "roller coaster" was demonstrated, where microscale particles in water were optically trapped and transported by a fiber helix. Tapered fiber loops and helices can find various applications ranging from on-the-fly characterization of integrated photonic devices to particle manipulation and sorting in microfluidics.

One-loop calculations in Supersymmetric Lattice QCD

NASA Astrophysics Data System (ADS)

Costa, M.; Panagopoulos, H.

2017-03-01

We study the self energies of all particles which appear in a lattice regularization of supersymmetric QCD (N = 1). We compute, perturbatively to one-loop, the relevant two-point Green's functions using both the dimensional and the lattice regularizations. Our lattice formulation employs the Wilson fermion acrion for the gluino and quark fields. The gauge group that we consider is SU(Nc) while the number of colors, Nc and the number of flavors, Nf , are kept as generic parameters. We have also searched for relations among the propagators which are computed from our one-loop results. We have obtained analytic expressions for the renormalization functions of the quark field (Zψ), gluon field (Zu), gluino field (Zλ) and squark field (ZA±). We present here results from dimensional regularization, relegating to a forthcoming publication [1] our results along with a more complete list of references. Part of the lattice study regards also the renormalization of quark bilinear operators which, unlike the nonsupersymmetric case, exhibit a rich pattern of operator mixing at the quantum level.

Cyclic Mario worlds — color-decomposition for one-loop QCD

NASA Astrophysics Data System (ADS)

Kälin, Gregor

2018-04-01

We present a new color decomposition for QCD amplitudes at one-loop level as a generalization of the Del Duca-Dixon-Maltoni and Johansson-Ochirov decomposition at tree level. Starting from a minimal basis of planar primitive amplitudes we write down a color decomposition that is free of linear dependencies among appearing primitive amplitudes or color factors. The conjectured decomposition applies to any number of quark flavors and is independent of the choice of gauge group and matter representation. The results also hold for higher-dimensional or supersymmetric extensions of QCD. We provide expressions for any number of external quark-antiquark pairs and gluons. [Figure not available: see fulltext.

RELAP5-3D Modeling of Heat Transfer Components (Intermediate Heat Exchanger and Helical-Coil Steam Generator) for NGNP Application

DOE Office of Scientific and Technical Information (OSTI.GOV)

N. A. Anderson; P. Sabharwall

2014-01-01

The Next Generation Nuclear Plant project is aimed at the research and development of a helium-cooled high-temperature gas reactor that could generate both electricity and process heat for the production of hydrogen. The heat from the high-temperature primary loop must be transferred via an intermediate heat exchanger to a secondary loop. Using RELAP5-3D, a model was developed for two of the heat exchanger options a printed-circuit heat exchanger and a helical-coil steam generator. The RELAP5-3D models were used to simulate an exponential decrease in pressure over a 20 second period. The results of this loss of coolant analysis indicate thatmore » heat is initially transferred from the primary loop to the secondary loop, but after the decrease in pressure in the primary loop the heat is transferred from the secondary loop to the primary loop. A high-temperature gas reactor model should be developed and connected to the heat transfer component to simulate other transients.« less

Leading-Color Fully Differential Two-Loop Soft Corrections to QCD Dipole Showers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dulat, Falko; Höche, Stefan; Prestel, Stefan

We compute the next-to-leading order corrections to soft-gluon radiation differentially in the one-emission phase space. We show that their contribution to the evolution of color dipoles can be obtained in a modified subtraction scheme, such that both one- and two-emission terms are amenable to Monte-Carlo integration. The two-loop cusp anomalous dimension is recovered naturally upon integration over the full phase space. We present two independent implementations of the new algorithm in the two event generators Pythia and Sherpa, and we compare the resulting fully differential simulation to the CMW scheme.

Helicity charging and eruption of magnetic flux from the Sun

NASA Technical Reports Server (NTRS)

Rust, David M.; Kumar, A.

1994-01-01

The ejection of helical toroidal fields from the solar atmosphere and their detection in interplanetary space are described. The discovery that solar magnetic fields are twisted and that they are segregated by hemisphere according to their chirality has important implications for the escape process. The roles played by erupting prominences, coronal mass ejections (CME's) and active region (AR) loops in expressing the escape of magnetic flux and helicity are discussed. Sporadic flux escape associated with filament eruptions accounts for less than one-tenth the flux loss. Azimuthal flux loss by CME's could account for more, but the major contributor to flux escape may be AR loop expansion. It is shown how the transfer of magnetic helicity from the sun's interior into emerged loops ('helicity charging') could be the effective driver of solar eruptions and of flux loss from the sun.

Lattice QCD analysis for relation between quark confinement and chiral symmetry breaking

DOE Office of Scientific and Technical Information (OSTI.GOV)

Doi, Takahiro M.; Suganuma, Hideo; Iritani, Takumi

2016-01-22

The Polyakov loop and the Dirac modes are connected via a simple analytical relation on the temporally odd-number lattice, where the temporal lattice size is odd with the normal (nontwisted) periodic boundary condition. Using this relation, we investigate the relation between quark confinement and chiral symmetry breaking in QCD. In this paper, we discuss the properties of this analytical relation and numerically investigate each Dirac-mode contribution to the Polyakov loop in both confinement and deconfinement phases at the quenched level. This relation indicates that low-lying Dirac modes have little contribution to the Polyakov loop, and we numerically confirmed this fact.more » From our analysis, it is suggested that there is no direct one-to-one corresponding between quark confinement and chiral symmetry breaking in QCD. Also, in the confinement phase, we numerically find that there is a new “positive/negative symmetry” in the Dirac-mode matrix elements of link-variable operator which appear in the relation and the Polyakov loop becomes zero because of this symmetry. In the deconfinement phase, this symmetry is broken and the Polyakov loop is non-zero.« less

Prediction of Long Loops with Embedded Secondary Structure using the Protein Local Optimization Program

PubMed Central

Miller, Edward B.; Murrett, Colleen S.; Zhu, Kai; Zhao, Suwen; Goldfeld, Dahlia A.; Bylund, Joseph H.; Friesner, Richard A.

2013-01-01

Robust homology modeling to atomic-level accuracy requires in the general case successful prediction of protein loops containing small segments of secondary structure. Further, as loop prediction advances to success with larger loops, the exclusion of loops containing secondary structure becomes awkward. Here, we extend the applicability of the Protein Local Optimization Program (PLOP) to loops up to 17 residues in length that contain either helical or hairpin segments. In general, PLOP hierarchically samples conformational space and ranks candidate loops with a high-quality molecular mechanics force field. For loops identified to possess α-helical segments, we employ an alternative dihedral library composed of (ϕ,ψ) angles commonly found in helices. The alternative library is searched over a user-specified range of residues that define the helical bounds. The source of these helical bounds can be from popular secondary structure prediction software or from analysis of past loop predictions where a propensity to form a helix is observed. Due to the maturity of our energy model, the lowest energy loop across all experiments can be selected with an accuracy of sub-Ångström RMSD in 80% of cases, 1.0 to 1.5 Å RMSD in 14% of cases, and poorer than 1.5 Å RMSD in 6% of cases. The effectiveness of our current methods in predicting hairpin-containing loops is explored with hairpins up to 13 residues in length and again reaching an accuracy of sub-Ångström RMSD in 83% of cases, 1.0 to 1.5 Å RMSD in 10% of cases, and poorer than 1.5 Å RMSD in 7% of cases. Finally, we explore the effect of an imprecise surrounding environment, in which side chains, but not the backbone, are initially in perturbed geometries. In these cases, loops perturbed to 3Å RMSD from the native environment were restored to their native conformation with sub-Ångström RMSD. PMID:23814507

N =4 supergravity next-to-maximally-helicity-violating six-point one-loop amplitude

NASA Astrophysics Data System (ADS)

Dunbar, David C.; Perkins, Warren B.

2016-12-01

We construct the six-point, next-to-maximally-helicity-violating one-loop amplitude in N =4 supergravity using unitarity and recursion. The use of recursion requires the introduction of rational descendants of the cut-constructible pieces of the amplitude and the computation of the nonstandard factorization terms arising from the loop integrals.

A dihydropyridine receptor alpha1s loop region critical for skeletal muscle contraction is intrinsically unstructured and binds to a SPRY domain of the type 1 ryanodine receptor.

PubMed

Cui, Yanfang; Tae, Han-Shen; Norris, Nicole C; Karunasekara, Yamuna; Pouliquin, Pierre; Board, Philip G; Dulhunty, Angela F; Casarotto, Marco G

2009-03-01

The II-III loop of the dihydropyridine receptor (DHPR) alpha(1s) subunit is a modulator of the ryanodine receptor (RyR1) Ca(2+) release channel in vitro and is essential for skeletal muscle contraction in vivo. Despite its importance, the structure of this loop has not been reported. We have investigated its structure using a suite of NMR techniques which revealed that the DHPR II-III loop is an intrinsically unstructured protein (IUP) and as such belongs to a burgeoning structural class of functionally important proteins. The loop does not possess a stable tertiary fold: it is highly flexible, with a strong N-terminal helix followed by nascent helical/turn elements and unstructured segments. Its residual structure is loosely globular with the N and C termini in close proximity. The unstructured nature of the II-III loop may allow it to easily modify its interaction with RyR1 following a surface action potential and thus initiate rapid Ca(2+) release and contraction. The in vitro binding partner for the II-III was investigated. The II-III loop interacts with the second of three structurally distinct SPRY domains in RyR1, whose function is unknown. This interaction occurs through two preformed N-terminal alpha-helical regions and a C-terminal hydrophobic element. The A peptide corresponding to the helical N-terminal region is a common probe of RyR function and binds to the same SPRY domain as the full II-III loop. Thus the second SPRY domain is an in vitro binding site for the II-III loop. The possible in vivo role of this region is discussed.

Higher order corrections to mixed QCD-EW contributions to Higgs boson production in gluon fusion

NASA Astrophysics Data System (ADS)

Bonetti, Marco; Melnikov, Kirill; Tancredi, Lorenzo

2018-03-01

We present an estimate of the next-to-leading-order (NLO) QCD corrections to mixed QCD-electroweak contributions to the Higgs boson production cross section in gluon fusion, combining the recently computed three-loop virtual corrections and the approximate treatment of real emission in the soft approximation. We find that the NLO QCD corrections to the mixed QCD-electroweak contributions are nearly identical to NLO QCD corrections to QCD Higgs production. Our result confirms an earlier estimate of these O (α αs2) effects by Anastasiou et al. [J. High Energy Phys. 04 (2009) 003, 10.1088/1126-6708/2009/04/003] and provides further support for the factorization approximation of QCD and electroweak corrections.

NLO QCD effective field theory analysis of W+W- production at the LHC including fermionic operators

NASA Astrophysics Data System (ADS)

Baglio, Julien; Dawson, Sally; Lewis, Ian M.

2017-10-01

We study the impact of anomalous gauge boson and fermion couplings on the production of W+W- pairs at the LHC. Helicity amplitudes are presented separately to demonstrate the sources of new physics contributions and the impact of QCD and electroweak corrections. The QCD corrections have important effects on the fits to anomalous couplings, in particular when one W boson is longitudinally polarized and the other is transversely polarized. In effective field theory language, we demonstrate that the dimension-6 approximation to constraining new physics effects in W+W- pair production fails at pT˜500 - 1000 GeV .

Gluonic transversity from lattice QCD

NASA Astrophysics Data System (ADS)

Detmold, W.; Shanahan, P. E.

2016-07-01

We present an exploratory study of the gluonic structure of the ϕ meson using lattice QCD (LQCD). This includes the first investigation of gluonic transversity via the leading moment of the twist-2 double-helicity-flip gluonic structure function Δ (x ,Q2). This structure function only exists for targets of spin J ≥1 and does not mix with quark distributions at leading twist, thereby providing a particularly clean probe of gluonic degrees of freedom. We also explore the gluonic analogue of the Soffer bound which relates the helicity flip and nonflip gluonic distributions, finding it to be saturated at the level of 80%. This work sets the stage for more complex LQCD studies of gluonic structure in the nucleon and in light nuclei where Δ (x ,Q2) is an "exotic glue" observable probing gluons in a nucleus not associated with individual nucleons.

γ5 in the four-dimensional helicity scheme

NASA Astrophysics Data System (ADS)

Gnendiger, C.; Signer, A.

2018-05-01

We investigate the regularization-scheme dependent treatment of γ5 in the framework of dimensional regularization, mainly focusing on the four-dimensional helicity scheme (fdh). Evaluating distinctive examples, we find that for one-loop calculations, the recently proposed four-dimensional formulation (fdf) of the fdh scheme constitutes a viable and efficient alternative compared to more traditional approaches. In addition, we extend the considerations to the two-loop level and compute the pseudoscalar form factors of quarks and gluons in fdh. We provide the necessary operator renormalization and discuss at a practical level how the complexity of intermediate calculational steps can be reduced in an efficient way.

Estimating loop length from CryoEM images at medium resolutions.

PubMed

McKnight, Andrew; Si, Dong; Al Nasr, Kamal; Chernikov, Andrey; Chrisochoides, Nikos; He, Jing

2013-01-01

De novo protein modeling approaches utilize 3-dimensional (3D) images derived from electron cryomicroscopy (CryoEM) experiments. The skeleton connecting two secondary structures such as α-helices represent the loop in the 3D image. The accuracy of the skeleton and of the detected secondary structures are critical in De novo modeling. It is important to measure the length along the skeleton accurately since the length can be used as a constraint in modeling the protein. We have developed a novel computational geometric approach to derive a simplified curve in order to estimate the loop length along the skeleton. The method was tested using fifty simulated density images of helix-loop-helix segments of atomic structures and eighteen experimentally derived density data from Electron Microscopy Data Bank (EMDB). The test using simulated density maps shows that it is possible to estimate within 0.5 Å of the expected length for 48 of the 50 cases. The experiments, involving eighteen experimentally derived CryoEM images, show that twelve cases have error within 2 Å. The tests using both simulated and experimentally derived images show that it is possible for our proposed method to estimate the loop length along the skeleton if the secondary structure elements, such as α-helices, can be detected accurately, and there is a continuous skeleton linking the α-helices.

On the loop approximation in nucleon QCD sum rules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Drukarev, E. G., E-mail: drukarev@thd.pnpi.spb.ru; Ryskin, M. G.; Sadovnikova, V. A.

There was a general belief that the nucleon QCD sum rules which include only the quark loops and thus contain only the condensates of dimension d = 3 and d = 4 have only a trivial solution. We demonstrate that there is also a nontrivial solution. We show that it can be treated as the lowest order approximation to the solution which includes the higher terms of the Operator Product Expansion. Inclusion of the radiative corrections improves the convergence of the series.

Consequences of non-uniformity in the stoichiometry of component fractions within one and two loops models of alpha-helical peptides

USDA-ARS?s Scientific Manuscript database

Atoms in biomolecular structures like alpha helices contain an array of distances and angles which include abundant multiple patterns of redundancies. Thus all peptides backbones contain the three atom sequence N-C*C, whereas the repeating set of a four atom sequences (N-C*C-N, C*-C-N-C*, and C-N-C...

All two-loop maximally helicity-violating amplitudes in multi-Regge kinematics from applied symbology

NASA Astrophysics Data System (ADS)

Prygarin, Alexander; Spradlin, Marcus; Vergu, Cristian; Volovich, Anastasia

2012-04-01

Recent progress on scattering amplitudes has benefited from the mathematical technology of symbols for efficiently handling the types of polylogarithm functions which frequently appear in multiloop computations. The symbol for all two-loop maximally helicity violating amplitudes in planar supersymmetric Yang-Mills theory is known, but explicit analytic formulas for the amplitudes are hard to come by except in special limits where things simplify, such as multi-Regge kinematics. By applying symbology we obtain a formula for the leading behavior of the imaginary part (the Mandelstam cut contribution) of this amplitude in multi-Regge kinematics for any number of gluons. Our result predicts a simple recursive structure which agrees with a direct Balitsky-Fadin-Kuraev-Lipatov computation carried out in a parallel publication.

An auto-inhibitory helix in CTP:phosphocholine cytidylyltransferase hijacks the catalytic residue and constrains a pliable, domain-bridging helix pair

PubMed Central

Ramezanpour, Mohsen; Lee, Jaeyong; Taneva, Svetla G.; Tieleman, D. Peter; Cornell, Rosemary B.

2018-01-01

The activity of CTP:phosphocholine cytidylyltransferase (CCT), a key enzyme in phosphatidylcholine synthesis, is regulated by reversible interactions of a lipid-inducible amphipathic helix (domain M) with membrane phospholipids. When dissociated from membranes, a portion of the M domain functions as an auto-inhibitory (AI) element to suppress catalysis. The AI helix from each subunit binds to a pair of α helices (αE) that extend from the base of the catalytic dimer to create a four-helix bundle. The bound AI helices make intimate contact with loop L2, housing a key catalytic residue, Lys122. The impacts of the AI helix on active-site dynamics and positioning of Lys122 are unknown. Extensive MD simulations with and without the AI helix revealed that backbone carbonyl oxygens at the point of contact between the AI helix and loop L2 can entrap the Lys122 side chain, effectively competing with the substrate, CTP. In silico, removal of the AI helices dramatically increased αE dynamics at a predicted break in the middle of these helices, enabling them to splay apart and forge new contacts with loop L2. In vitro cross-linking confirmed the reorganization of the αE element upon membrane binding of the AI helix. Moreover, when αE bending was prevented by disulfide engineering, CCT activation by membrane binding was thwarted. These findings suggest a novel two-part auto-inhibitory mechanism for CCT involving capture of Lys122 and restraint of the pliable αE helices. We propose that membrane binding enables bending of the αE helices, bringing the active site closer to the membrane surface. PMID:29519816

On the small-x behavior of the orbital angular momentum distributions in QCD

NASA Astrophysics Data System (ADS)

Hatta, Yoshitaka; Yang, Dong-Jing

2018-06-01

We present the numerical solution of the leading order QCD evolution equation for the orbital angular momentum distributions of quarks and gluons and discuss its implications for the nucleon spin sum rule. We observe that at small-x, the gluon helicity and orbital angular momentum distributions are roughly of the same magnitude but with opposite signs, indicating a significant cancellation between them. A similar cancellation occurs also in the quark sector. We explain analytically the reason for this cancellation.

NLO QCD effective field theory analysis of W +W - production at the LHC including fermionic operators

DOE PAGES

Baglio, Julien; Dawson, Sally; Lewis, Ian M.

2017-10-03

In this paper, we study the impact of anomalous gauge boson and fermion couplings on the production of W +W - pairs at the LHC. Helicity amplitudes are presented separately to demonstrate the sources of new physics contributions and the impact of QCD and electroweak corrections. The QCD corrections have important effects on the fits to anomalous couplings, in particular when one W boson is longitudinally polarized and the other is transversely polarized. In effective field theory language, we demonstrate that the dimension-6 approximation to constraining new physics effects in W +W - pair production fails at p T ~more » 500 - 1000 GeV.« less

NLO QCD effective field theory analysis of W +W - production at the LHC including fermionic operators

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baglio, Julien; Dawson, Sally; Lewis, Ian M.

In this paper, we study the impact of anomalous gauge boson and fermion couplings on the production of W +W - pairs at the LHC. Helicity amplitudes are presented separately to demonstrate the sources of new physics contributions and the impact of QCD and electroweak corrections. The QCD corrections have important effects on the fits to anomalous couplings, in particular when one W boson is longitudinally polarized and the other is transversely polarized. In effective field theory language, we demonstrate that the dimension-6 approximation to constraining new physics effects in W +W - pair production fails at p T ~more » 500 - 1000 GeV.« less

Charged-pion cross sections and double-helicity asymmetries in polarized p + p collisions at √s = 200 GeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adare, A.; Aidala, C.; Ajitanand, N. N.

2015-02-02

We present midrapidity charged-pion invariant cross sections, the ratio of the π⁻ to π⁺ cross sections and the charge-separated double-spin asymmetries in polarized p+p collisions at √s = 200 GeV. While the cross section measurements are consistent within the errors of next-to-leadingorder (NLO) perturbative quantum chromodynamics predictions (pQCD), the same calculations over estimate the ratio of the charged-pion cross sections. This discrepancy arises from the cancellation of the substantial systematic errors associated with the NLO-pQCD predictions in the ratio and highlights the constraints these data will place on flavor dependent pion fragmentation functions. Thus, the charge-separated pion asymmetries presented heremore » sample an x range of ~0.03–0.16 and provide unique information on the sign of the gluon-helicity distribution.« less

Charged-pion cross sections and double-helicity asymmetries in polarized p +p collisions at √{s }=200 GeV

NASA Astrophysics Data System (ADS)

Adare, A.; Aidala, C.; Ajitanand, N. N.; Akiba, Y.; Akimoto, R.; Al-Ta'Ani, H.; Alexander, J.; Andrews, K. R.; Angerami, A.; Aoki, K.; Apadula, N.; Appelt, E.; Aramaki, Y.; Armendariz, R.; Aschenauer, E. C.; Atomssa, E. T.; Awes, T. C.; Azmoun, B.; Babintsev, V.; Bai, M.; Bannier, B.; Barish, K. N.; Bassalleck, B.; Basye, A. T.; Bathe, S.; Baublis, V.; Baumann, C.; Bazilevsky, A.; Belmont, R.; Ben-Benjamin, J.; Bennett, R.; Blau, D. S.; Bok, J. S.; Boyle, K.; Brooks, M. L.; Broxmeyer, D.; Buesching, H.; Bumazhnov, V.; Bunce, G.; Butsyk, S.; Campbell, S.; Castera, P.; Chen, C.-H.; Chi, C. Y.; Chiu, M.; Choi, I. J.; Choi, J. B.; Choudhury, R. K.; Christiansen, P.; Chujo, T.; Chvala, O.; Cianciolo, V.; Citron, Z.; Cole, B. A.; Conesa Del Valle, Z.; Connors, M.; Csanád, M.; Csörgő, T.; Dairaku, S.; Datta, A.; David, G.; Dayananda, M. K.; Denisov, A.; Deshpande, A.; Desmond, E. J.; Dharmawardane, K. V.; Dietzsch, O.; Dion, A.; Donadelli, M.; Drapier, O.; Drees, A.; Drees, K. A.; Durham, J. M.; Durum, A.; D'Orazio, L.; Efremenko, Y. V.; Engelmore, T.; Enokizono, A.; En'yo, H.; Esumi, S.; Fadem, B.; Fields, D. E.; Finger, M.; Finger, M.; Fleuret, F.; Fokin, S. L.; Frantz, J. E.; Franz, A.; Frawley, A. D.; Fukao, Y.; Fusayasu, T.; Gal, C.; Garishvili, I.; Giordano, F.; Glenn, A.; Gong, X.; Gonin, M.; Goto, Y.; Granier de Cassagnac, R.; Grau, N.; Greene, S. V.; Grosse Perdekamp, M.; Gunji, T.; Guo, L.; Gustafsson, H.-Å.; Haggerty, J. S.; Hahn, K. I.; Hamagaki, H.; Hamblen, J.; Han, R.; Hanks, J.; Harper, C.; Hashimoto, K.; Haslum, E.; Hayano, R.; He, X.; Hemmick, T. K.; Hester, T.; Hill, J. C.; Hollis, R. S.; Holzmann, W.; Homma, K.; Hong, B.; Horaguchi, T.; Hori, Y.; Hornback, D.; Huang, S.; Ichihara, T.; Ichimiya, R.; Iinuma, H.; Ikeda, Y.; Imai, K.; Inaba, M.; Iordanova, A.; Isenhower, D.; Ishihara, M.; Issah, M.; Ivanischev, D.; Iwanaga, Y.; Jacak, B. V.; Jia, J.; Jiang, X.; John, D.; Johnson, B. M.; Jones, T.; Joo, K. S.; Jouan, D.; Kamin, J.; Kaneti, S.; Kang, B. H.; Kang, J. H.; Kang, J. S.; Kapustinsky, J.; Karatsu, K.; Kasai, M.; Kawall, D.; Kazantsev, A. V.; Kempel, T.; Khanzadeev, A.; Kijima, K. M.; Kim, B. I.; Kim, D. J.; Kim, E.-J.; Kim, Y.-J.; Kim, Y. K.; Kinney, E.; Kiss, Á.; Kistenev, E.; Kleinjan, D.; Kline, P.; Kochenda, L.; Komkov, B.; Konno, M.; Koster, J.; Kotov, D.; Král, A.; Kunde, G. J.; Kurita, K.; Kurosawa, M.; Kwon, Y.; Kyle, G. S.; Lacey, R.; Lai, Y. S.; Lajoie, J. G.; Lebedev, A.; Lee, D. M.; Lee, J.; Lee, K. B.; Lee, K. S.; Lee, S. H.; Lee, S. R.; Leitch, M. J.; Leite, M. A. L.; Li, X.; Lim, S. H.; Linden Levy, L. A.; Liu, H.; Liu, M. X.; Love, B.; Lynch, D.; Maguire, C. F.; Makdisi, Y. I.; Manion, A.; Manko, V. I.; Mannel, E.; Mao, Y.; Masui, H.; McCumber, M.; McGaughey, P. L.; McGlinchey, D.; McKinney, C.; Means, N.; Mendoza, M.; Meredith, B.; Miake, Y.; Mibe, T.; Mignerey, A. C.; Miki, K.; Milov, A.; Mitchell, J. T.; Miyachi, Y.; Mohanty, A. K.; Moon, H. J.; Morino, Y.; Morreale, A.; Morrison, D. P.; Motschwiller, S.; Moukhanova, T. V.; Murakami, T.; Murata, J.; Nagamiya, S.; Nagle, J. L.; Naglis, M.; Nagy, M. I.; Nakagawa, I.; Nakamiya, Y.; Nakamura, K. R.; Nakamura, T.; Nakano, K.; Newby, J.; Nguyen, M.; Nihashi, M.; Nouicer, R.; Nyanin, A. S.; Oakley, C.; O'Brien, E.; Ogilvie, C. A.; Oka, M.; Okada, K.; Oskarsson, A.; Ouchida, M.; Ozawa, K.; Pak, R.; Pantuev, V.; Papavassiliou, V.; Park, B. H.; Park, I. H.; Park, S. K.; Pate, S. F.; Patel, L.; Pei, H.; Peng, J.-C.; Pereira, H.; Peressounko, D. Yu.; Petti, R.; Pinkenburg, C.; Pisani, R. P.; Proissl, M.; Purschke, M. L.; Qu, H.; Rak, J.; Ravinovich, I.; Read, K. F.; Reygers, K.; Riabov, V.; Riabov, Y.; Richardson, E.; Roach, D.; Roche, G.; Rolnick, S. D.; Rosati, M.; Rosendahl, S. S. E.; Rubin, J. G.; Sahlmueller, B.; Saito, N.; Sakaguchi, T.; Samsonov, V.; Sano, S.; Sarsour, M.; Sato, T.; Savastio, M.; Sawada, S.; Sedgwick, K.; Seidl, R.; Seto, R.; Sharma, D.; Shein, I.; Shibata, T.-A.; Shigaki, K.; Shim, H. H.; Shimomura, M.; Shoji, K.; Shukla, P.; Sickles, A.; Silva, C. L.; Silvermyr, D.; Silvestre, C.; Sim, K. S.; Singh, B. K.; Singh, C. P.; Singh, V.; Slunečka, M.; Sodre, T.; Soltz, R. A.; Sondheim, W. E.; Sorensen, S. P.; Sourikova, I. V.; Stankus, P. W.; Stenlund, E.; Stoll, S. P.; Sugitate, T.; Sukhanov, A.; Sun, J.; Sziklai, J.; Takagui, E. M.; Takahara, A.; Taketani, A.; Tanabe, R.; Tanaka, Y.; Taneja, S.; Tanida, K.; Tannenbaum, M. J.; Tarafdar, S.; Taranenko, A.; Tennant, E.; Themann, H.; Thomas, D.; Togawa, M.; Tomášek, L.; Tomášek, M.; Torii, H.; Towell, R. S.; Tserruya, I.; Tsuchimoto, Y.; Utsunomiya, K.; Vale, C.; van Hecke, H. W.; Vazquez-Zambrano, E.; Veicht, A.; Velkovska, J.; Vértesi, R.; Virius, M.; Vossen, A.; Vrba, V.; Vznuzdaev, E.; Wang, X. R.; Watanabe, D.; Watanabe, K.; Watanabe, Y.; Watanabe, Y. S.; Wei, F.; Wei, R.; Wessels, J.; White, S. N.; Winter, D.; Woody, C. L.; Wright, R. M.; Wysocki, M.; Yamaguchi, Y. L.; Yang, R.; Yanovich, A.; Ying, J.; Yokkaichi, S.; Yoo, J. S.; You, Z.; Young, G. R.; Younus, I.; Yushmanov, I. E.; Zajc, W. A.; Zelenski, A.; Zhou, S.; Phenix Collaboration

2015-02-01

We present midrapidity charged-pion invariant cross sections, the ratio of the π- to π+ cross sections and the charge-separated double-spin asymmetries in polarized p +p collisions at √{s }=200 GeV . While the cross section measurements are consistent within the errors of next-to-leading-order (NLO) perturbative quantum chromodynamics predictions (pQCD), the same calculations overestimate the ratio of the charged-pion cross sections. This discrepancy arises from the cancellation of the substantial systematic errors associated with the NLO-pQCD predictions in the ratio and highlights the constraints these data will place on flavor-dependent pion fragmentation functions. The charge-separated pion asymmetries presented here sample an x range of ˜0.03 - 0.16 and provide unique information on the sign of the gluon-helicity distribution.

The Structure of Coronal Loops

NASA Technical Reports Server (NTRS)

Antiochos, Spiro K.

2009-01-01

It is widely believed that the simple coronal loops observed by XUV imagers, such as EIT, TRACE, or XRT, actually have a complex internal structure consisting of many (perhaps hundreds) of unresolved, interwoven "strands". According to the nanoflare model, photospheric motions tangle the strands, causing them to reconnect and release the energy required to produce the observed loop plasma. Although the strands, themselves, are unresolved by present-generation imagers, there is compelling evidence for their existence and for the nanoflare model from analysis of loop intensities and temporal evolution. A problem with this scenario is that, although reconnection can eliminate some of the strand tangles, it cannot destroy helicity, which should eventually build up to observable scales. we consider, therefore, the injection and evolution of helicity by the nanoflare process and its implications for the observed structure of loops and the large-scale corona. we argue that helicity does survive and build up to observable levels, but on spatial and temporal scales larger than those of coronal loops. we discuss the implications of these results for coronal loops and the corona, in general .

Neutral and charged scalar mesons, pseudoscalar mesons, and diquarks in magnetic fields

NASA Astrophysics Data System (ADS)

Liu, Hao; Wang, Xinyang; Yu, Lang; Huang, Mei

2018-04-01

We investigate both (pseudo)scalar mesons and diquarks in the presence of external magnetic field in the framework of the two-flavored Nambu-Jona-Lasinio (NJL) model, where mesons and diquarks are constructed by infinite sum of quark-loop chains by using random phase approximation. The polarization function of the quark-loop is calculated to the leading order of 1 /Nc expansion by taking the quark propagator in the Landau level representation. We systematically investigate the masses behaviors of scalar σ meson, neutral and charged pions as well as the scalar diquarks, with respect to the magnetic field strength at finite temperature and chemical potential. It is shown that the numerical results of both neutral and charged pions are consistent with the lattice QCD simulations. The mass of the charge neutral pion keeps almost a constant under the magnetic field, which is preserved by the remnant symmetry of QCD ×QED in the vacuum. The mass of the charge neutral scalar σ is around two times quark mass and increases with the magnetic field due to the magnetic catalysis effect, which is an typical example showing that the polarized internal quark structure cannot be neglected when we consider the meson properties under magnetic field. For the charged particles, the one quark-antiquark loop contribution to the charged π± increases essentially with the increase of magnetic fields due to the magnetic catalysis of the polarized quarks. However, the one quark-quark loop contribution to the scalar diquark mass is negative comparing with the point-particle result and the loop effect is small.

On the Mysterious Propulsion of Synechococcus

PubMed Central

Ehlers, Kurt; Oster, George

2012-01-01

We propose a model for the self-propulsion of the marine bacterium Synechococcus utilizing a continuous looped helical track analogous to that found in Myxobacteria [1]. In our model cargo-carrying protein motors, driven by proton-motive force, move along a continuous looped helical track. The movement of the cargo creates surface distortions in the form of small amplitude traveling ridges along the S-layer above the helical track. The resulting fluid motion adjacent to the helical ribbon provides the propulsive thrust. A variation on the helical rotor model of [1] allows the motors to be anchored to the peptidoglycan layer, where they drive rotation of the track creating traveling helical waves along the S-layer. We derive expressions relating the swimming speed to the amplitude, wavelength, and velocity of the surface waves induced by the helical rotor, and show that they fall in reasonable ranges to explain the velocity and rotation rate of swimming Synechococcus. PMID:22567124

Relating quark confinement and chiral symmetry breaking in QCD

NASA Astrophysics Data System (ADS)

Suganuma, Hideo; Doi, Takahiro M.; Redlich, Krzysztof; Sasaki, Chihiro

2017-12-01

We study the relation between quark confinement and chiral symmetry breaking in QCD. Using lattice QCD formalism, we analytically express the various ‘confinement indicators’, such as the Polyakov loop, its fluctuations, the Wilson loop, the inter-quark potential and the string tension, in terms of the Dirac eigenmodes. In the Dirac spectral representation, there appears a power of the Dirac eigenvalue {λ }n such as {λ }n{Nt-1}, which behaves as a reduction factor for small {λ }n. Consequently, since this reduction factor cannot be cancelled, the low-lying Dirac eigenmodes give negligibly small contribution to the confinement quantities, while they are essential for chiral symmetry breaking. These relations indicate that there is no direct one-to-one correspondence between confinement and chiral symmetry breaking in QCD. In other words, there is some independence of quark confinement from chiral symmetry breaking, which can generally lead to different transition temperatures/densities for deconfinement and chiral restoration. We also investigate the Polyakov loop in terms of the eigenmodes of the Wilson, the clover and the domain-wall fermion kernels, and find similar results. The independence of quark confinement from chiral symmetry breaking seems to be natural, because confinement is realized independently of quark masses and heavy quarks are also confined even without the chiral symmetry.

Electroexcitation of nucleon resonances

DOE Office of Scientific and Technical Information (OSTI.GOV)

Inna Aznauryan, Volker D. Burkert

2012-01-01

We review recent progress in the investigation of the electroexcitation of nucleon resonances, both in experiment and in theory. The most accurate results have been obtained for the electroexcitation amplitudes of the four lowest excited states, which have been measured in a range of Q2 up to 8 and 4.5 GeV2 for the Delta(1232)P33, N(1535)S11 and N(1440)P11, N(1520)D13, respectively. These results have been confronted with calculations based on lattice QCD, large-Nc relations, perturbative QCD (pQCD), and QCD-inspired models. The amplitudes for the Delta(1232) indicate large pion-cloud contributions at low Q2 and don't show any sign of approaching the pQCD regimemore » for Q2<7 GeV2. Measured for the first time, the electroexcitation amplitudes of the Roper resonance, N(1440)P11, provide strong evidence for this state as a predominantly radial excitation of a three-quark (3q) ground state, with additional non-3-quark contributions needed to describe the low Q2 behavior of the amplitudes. The longitudinal transition amplitude for the N(1535)S11 was determined and has become a challenge for quark models. Explanations may require large meson-cloud contributions or alternative representations of this state. The N(1520)D13 clearly shows the rapid changeover from helicity-3/2 dominance at the real photon point to helicity-1/2 dominance at Q2 > 0.5 GeV2, confirming a long-standing prediction of the constituent quark model. The interpretation of the moments of resonance transition form factors in terms of transition transverse charge distributions in infinite momentum frame is presented.« less

Renormalization group invariance and optimal QCD renormalization scale-setting: a key issues review.

PubMed

Wu, Xing-Gang; Ma, Yang; Wang, Sheng-Quan; Fu, Hai-Bing; Ma, Hong-Hao; Brodsky, Stanley J; Mojaza, Matin

2015-12-01

A valid prediction for a physical observable from quantum field theory should be independent of the choice of renormalization scheme--this is the primary requirement of renormalization group invariance (RGI). Satisfying scheme invariance is a challenging problem for perturbative QCD (pQCD), since a truncated perturbation series does not automatically satisfy the requirements of the renormalization group. In a previous review, we provided a general introduction to the various scale setting approaches suggested in the literature. As a step forward, in the present review, we present a discussion in depth of two well-established scale-setting methods based on RGI. One is the 'principle of maximum conformality' (PMC) in which the terms associated with the β-function are absorbed into the scale of the running coupling at each perturbative order; its predictions are scheme and scale independent at every finite order. The other approach is the 'principle of minimum sensitivity' (PMS), which is based on local RGI; the PMS approach determines the optimal renormalization scale by requiring the slope of the approximant of an observable to vanish. In this paper, we present a detailed comparison of the PMC and PMS procedures by analyzing two physical observables R(e+e-) and [Formula: see text] up to four-loop order in pQCD. At the four-loop level, the PMC and PMS predictions for both observables agree within small errors with those of conventional scale setting assuming a physically-motivated scale, and each prediction shows small scale dependences. However, the convergence of the pQCD series at high orders, behaves quite differently: the PMC displays the best pQCD convergence since it eliminates divergent renormalon terms; in contrast, the convergence of the PMS prediction is questionable, often even worse than the conventional prediction based on an arbitrary guess for the renormalization scale. PMC predictions also have the property that any residual dependence on the choice of initial scale is highly suppressed even for low-order predictions. Thus the PMC, based on the standard RGI, has a rigorous foundation; it eliminates an unnecessary systematic error for high precision pQCD predictions and can be widely applied to virtually all high-energy hadronic processes, including multi-scale problems.

Renormalization group invariance and optimal QCD renormalization scale-setting: a key issues review

NASA Astrophysics Data System (ADS)

Wu, Xing-Gang; Ma, Yang; Wang, Sheng-Quan; Fu, Hai-Bing; Ma, Hong-Hao; Brodsky, Stanley J.; Mojaza, Matin

2015-12-01

A valid prediction for a physical observable from quantum field theory should be independent of the choice of renormalization scheme—this is the primary requirement of renormalization group invariance (RGI). Satisfying scheme invariance is a challenging problem for perturbative QCD (pQCD), since a truncated perturbation series does not automatically satisfy the requirements of the renormalization group. In a previous review, we provided a general introduction to the various scale setting approaches suggested in the literature. As a step forward, in the present review, we present a discussion in depth of two well-established scale-setting methods based on RGI. One is the ‘principle of maximum conformality’ (PMC) in which the terms associated with the β-function are absorbed into the scale of the running coupling at each perturbative order; its predictions are scheme and scale independent at every finite order. The other approach is the ‘principle of minimum sensitivity’ (PMS), which is based on local RGI; the PMS approach determines the optimal renormalization scale by requiring the slope of the approximant of an observable to vanish. In this paper, we present a detailed comparison of the PMC and PMS procedures by analyzing two physical observables R e+e- and Γ(H\\to b\\bar{b}) up to four-loop order in pQCD. At the four-loop level, the PMC and PMS predictions for both observables agree within small errors with those of conventional scale setting assuming a physically-motivated scale, and each prediction shows small scale dependences. However, the convergence of the pQCD series at high orders, behaves quite differently: the PMC displays the best pQCD convergence since it eliminates divergent renormalon terms; in contrast, the convergence of the PMS prediction is questionable, often even worse than the conventional prediction based on an arbitrary guess for the renormalization scale. PMC predictions also have the property that any residual dependence on the choice of initial scale is highly suppressed even for low-order predictions. Thus the PMC, based on the standard RGI, has a rigorous foundation; it eliminates an unnecessary systematic error for high precision pQCD predictions and can be widely applied to virtually all high-energy hadronic processes, including multi-scale problems.

Algorithms for Disconnected Diagrams in Lattice QCD

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gambhir, Arjun Singh; Stathopoulos, Andreas; Orginos, Konstantinos

2016-11-01

Computing disconnected diagrams in Lattice QCD (operator insertion in a quark loop) entails the computationally demanding problem of taking the trace of the all to all quark propagator. We first outline the basic algorithm used to compute a quark loop as well as improvements to this method. Then, we motivate and introduce an algorithm based on the synergy between hierarchical probing and singular value deflation. We present results for the chiral condensate using a 2+1-flavor clover ensemble and compare estimates of the nucleon charges with the basic algorithm.

Quenching parameter in a holographic thermal QCD

NASA Astrophysics Data System (ADS)

Patra, Binoy Krishna; Arya, Bhaskar

2017-01-01

We have calculated the quenching parameter, q ˆ in a model-independent way using the gauge-gravity duality. In earlier calculations, the geometry in the gravity side at finite temperature was usually taken as the pure AdS black hole metric for which the dual gauge theory becomes conformally invariant unlike QCD. Therefore we use a metric which incorporates the fundamental quarks by embedding the coincident D7 branes in the Klebanov-Tseytlin background and a finite temperature is switched on by inserting a black hole into the background, known as OKS-BH metric. Further inclusion of an additional UV cap to the metric prepares the dual gauge theory to run similar to thermal QCD. Moreover q ˆ is usually defined in the literature from the Glauber model perturbative QCD evaluation of the Wilson loop, which has no reasons to hold if the coupling is large and is thus against the main idea of gauge-gravity duality. Thus we use an appropriate definition of q ˆ : q ˆ L- = 1 /L2, where L is the separation for which the Wilson loop is equal to some specific value. The above two refinements cause q ˆ to vary with the temperature as T4 always and to depend linearly on the light-cone time L- with an additional (1 /L-) correction term in the short-distance limit whereas in the long-distance limit, q ˆ depends only linearly on L- with no correction term. These observations agree with other holographic calculations directly or indirectly.

One-loop corrections to light cone wave functions: The dipole picture DIS cross section

NASA Astrophysics Data System (ADS)

Hänninen, H.; Lappi, T.; Paatelainen, R.

2018-06-01

We develop methods to perform loop calculations in light cone perturbation theory using a helicity basis, refining the method introduced in our earlier work. In particular this includes implementing a consistent way to contract the four-dimensional tensor structures from the helicity vectors with d-dimensional tensors arising from loop integrals, in a way that can be fully automatized. We demonstrate this explicitly by calculating the one-loop correction to the virtual photon to quark-antiquark dipole light cone wave function. This allows us to calculate the deep inelastic scattering cross section in the dipole formalism to next-to-leading order accuracy. Our results, obtained using the four dimensional helicity scheme, agree with the recent calculation by Beuf using conventional dimensional regularization, confirming the regularization scheme independence of this cross section.

Evanescent effects can alter ultraviolet divergences in quantum gravity without physical consequences

DOE PAGES

Bern, Zvi; Cheung, Clifford; Chi, Huan -Hang; ...

2015-11-17

Evanescent operators such as the Gauss-Bonnet term have vanishing perturbative matrix elements in exactly D = 4 dimensions. Similarly, evanescent fields do not propagate in D = 4; a three-form field is in this class, since it is dual to a cosmological-constant contribution. In this Letter, we show that evanescent operators and fields modify the leading ultraviolet divergence in pure gravity. To analyze the divergence, we compute the two-loop identical-helicity four-graviton amplitude and determine the coefficient of the associated (nonevanescent) R 3 counterterm studied long ago by Goroff and Sagnotti. We compare two pairs of theories that are dual inmore » D = 4: gravity coupled to nothing or to three-form matter, and gravity coupled to zero-form or to two-form matter. Duff and van Nieuwenhuizen showed that, curiously, the one-loop trace anomaly—the coefficient of the Gauss-Bonnet operator—changes under p-form duality transformations. In addition, we concur and also find that the leading R 3 divergence changes under duality transformations. Nevertheless, in both cases, the physical renormalized two-loop identical-helicity four-graviton amplitude can be chosen to respect duality. In particular, its renormalization-scale dependence is unaltered.« less

Evanescent Effects can Alter Ultraviolet Divergences in Quantum Gravity without Physical Consequences.

PubMed

Bern, Zvi; Cheung, Clifford; Chi, Huan-Hang; Davies, Scott; Dixon, Lance; Nohle, Josh

2015-11-20

Evanescent operators such as the Gauss-Bonnet term have vanishing perturbative matrix elements in exactly D=4 dimensions. Similarly, evanescent fields do not propagate in D=4; a three-form field is in this class, since it is dual to a cosmological-constant contribution. In this Letter, we show that evanescent operators and fields modify the leading ultraviolet divergence in pure gravity. To analyze the divergence, we compute the two-loop identical-helicity four-graviton amplitude and determine the coefficient of the associated (nonevanescent) R^{3} counterterm studied long ago by Goroff and Sagnotti. We compare two pairs of theories that are dual in D=4: gravity coupled to nothing or to three-form matter, and gravity coupled to zero-form or to two-form matter. Duff and van Nieuwenhuizen showed that, curiously, the one-loop trace anomaly-the coefficient of the Gauss-Bonnet operator-changes under p-form duality transformations. We concur and also find that the leading R^{3} divergence changes under duality transformations. Nevertheless, in both cases, the physical renormalized two-loop identical-helicity four-graviton amplitude can be chosen to respect duality. In particular, its renormalization-scale dependence is unaltered.

Scattering of glue by glue on the light-cone worldsheet: Helicity nonconserving amplitudes

NASA Astrophysics Data System (ADS)

Chakrabarti, D.; Qiu, J.; Thorn, C. B.

2005-09-01

We give the light-cone gauge calculation of the one-loop on-shell scattering amplitudes for gluon-gluon scattering which violate helicity conservation. We regulate infrared divergences by discretizing the p+ integrations, omitting the terms with p+=0. Collinear divergences are absent diagram by diagram for the helicity nonconserving amplitudes. We also employ a novel ultraviolet regulator that is natural for the light-cone worldsheet description of planar Feynman diagrams. We show that these regulators give the known answers for the helicity nonconserving one-loop amplitudes, which do not suffer from the usual infrared vagaries of massless particle scattering. For the maximal helicity violating process we elucidate the physics of the remarkable fact that the loop momentum integrand for the on-shell Green function associated with this process, with a suitable momentum routing of the different contributing topologies, is identically zero. We enumerate the counterterms that must be included to give Lorentz covariant results to this order, and we show that they can be described locally in the light-cone worldsheet formulation of the sum of planar diagrams.

Restoration of rotational symmetry in the continuum limit of lattice field theories

NASA Astrophysics Data System (ADS)

Davoudi, Zohreh; Savage, Martin J.

2012-09-01

We explore how rotational invariance is systematically recovered from calculations on hyper-cubic lattices through the use of smeared lattice operators that smoothly evolve into continuum operators with definite angular momentum as the lattice-spacing is reduced. Perturbative calculations of the angular momentum violation associated with such operators at tree level and at one loop are presented in λϕ4 theory and QCD. Contributions from these operators that violate rotational invariance occur at tree-level, with coefficients that are suppressed by O(a2) in the continuum limit. Quantum loops do not modify this behavior in λϕ4, nor in QCD if the gauge-fields are smeared over a comparable spatial region. Consequently, the use of this type of operator should, in principle, allow for Lattice QCD calculations of the higher moments of the hadron structure functions.

Smeared quasidistributions in perturbation theory

NASA Astrophysics Data System (ADS)

Monahan, Christopher

2018-03-01

Quasi- and pseudodistributions provide a new approach to determining parton distribution functions from first principles' calculations of QCD. Here, I calculate the flavor nonsinglet unpolarized quasidistribution at one loop in perturbation theory, using the gradient flow to remove ultraviolet divergences. I demonstrate that, as expected, the gradient flow does not change the infrared structure of the quasidistribution at one loop and use the results to match the smeared matrix elements to those in the MS ¯ scheme. This matching calculation is required to relate numerical results obtained from nonperturbative lattice QCD computations to light-front parton distribution functions extracted from global analyses of experimental data.

Radiative improvement of the lattice nonrelativistic QCD action using the background field method and application to the hyperfine splitting of quarkonium states.

PubMed

Hammant, T C; Hart, A G; von Hippel, G M; Horgan, R R; Monahan, C J

2011-09-09

We present the first application of the background field method to nonrelativistic QCD (NRQCD) on the lattice in order to determine the one-loop radiative corrections to the coefficients of the NRQCD action in a manifestly gauge-covariant manner. The coefficients of the σ·B term in the NRQCD action and the four-fermion spin-spin interaction are computed at the one-loop level; the resulting shift of the hyperfine splitting of bottomonium is found to bring the lattice predictions in line with experiment.

QCD Resummation for Single Spin Asymmetries

NASA Astrophysics Data System (ADS)

Kang, Zhong-Bo; Xiao, Bo-Wen; Yuan, Feng

2011-10-01

We study the transverse momentum dependent factorization for single spin asymmetries in Drell-Yan and semi-inclusive deep inelastic scattering processes at one-loop order. The next-to-leading order hard factors are calculated in the Ji-Ma-Yuan factorization scheme. We further derive the QCD resummation formalisms for these observables following the Collins-Soper-Sterman method. The results are expressed in terms of the collinear correlation functions from initial and/or final state hadrons coupled with the Sudakov form factor containing all order soft-gluon resummation effects. The scheme-independent coefficients are calculated up to one-loop order.

QCD Resummation for Single Spin Asymmetries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kang Z.; Xiao, Bo-Wen; Yuan, Feng

We study the transverse momentum dependent factorization for single spin asymmetries in Drell-Yan and semi-inclusive deep inelastic scattering processes at one-loop order. The next-to-leading order hard factors are calculated in the Ji-Ma-Yuan factorization scheme. We further derive the QCD resummation formalisms for these observables following the Collins-Soper-Sterman method. The results are expressed in terms of the collinear correlation functions from initial and/or final state hadrons coupled with the Sudakov form factor containing all order soft-gluon resummation effects. The scheme-independent coefficients are calculated up to one-loop order.

Polyakov loop and the hadron resonance gas model.

PubMed

Megías, E; Arriola, E Ruiz; Salcedo, L L

2012-10-12

The Polyakov loop has been used repeatedly as an order parameter in the deconfinement phase transition in QCD. We argue that, in the confined phase, its expectation value can be represented in terms of hadronic states, similarly to the hadron resonance gas model for the pressure. Specifically, L(T)≈1/2[∑(α)g(α)e(-Δ(α)/T), where g(α) are the degeneracies and Δ(α) are the masses of hadrons with exactly one heavy quark (the mass of the heavy quark itself being subtracted). We show that this approximate sum rule gives a fair description of available lattice data with N(f)=2+1 for temperatures in the range 150 MeV

Architecture of a Diels-Alderase ribozyme with a preformed catalytic pocket.

PubMed

Keiper, Sonja; Bebenroth, Dirk; Seelig, Burckhard; Westhof, Eric; Jäschke, Andres

2004-09-01

Artificial ribozymes catalyze a variety of chemical reactions. Their structures and reaction mechanisms are largely unknown. We have analyzed a ribozyme catalyzing Diels-Alder cycloaddition reactions by comprehensive mutation analysis and a variety of probing techniques. New tertiary interactions involving base pairs between nucleotides of the 5' terminus and a large internal loop forming a pseudoknot fold were identified. The probing data indicate a preformed tertiary structure that shows no major changes on substrate or product binding. Based on these observations, a molecular architecture featuring a Y-shaped arrangement is proposed. The tertiary structure is formed in a rather unusual way; that is, the opposite sides of the asymmetric internal loop are clamped by the four 5'-terminal nucleotides, forming two adjacent two base-pair helices. It is proposed that the catalytic pocket is formed by a wedge within one of these helices.

Comparison of confinement in resistive-shell reversed-field pinch devices with two different magnetic shell penetration times

NASA Astrophysics Data System (ADS)

Gravestijn, R. M.; Drake, J. R.; Hedqvist, A.; Rachlew, E.

2004-01-01

A loop voltage is required to sustain the reversed-field pinch (RFP) equilibrium. The configuration is characterized by redistribution of magnetic helicity but with the condition that the total helicity is maintained constant. The magnetic field shell penetration time, tgrs, has a critical role in the stability and performance of the RFP. Confinement in the EXTRAP device has been studied with two values of tgrs, first (EXTRAP-T2) with tgrs of the order of the typical relaxation cycle timescale and then (EXTRAP-T2R) with tgrs much longer than the relaxation cycle timescale, but still much shorter than the pulse length. Plasma parameters show significant improvements in confinement in EXTRAP-T2R. The typical loop voltage required to sustain comparable electron poloidal beta values is a factor of 3 lower in the EXTRAP-T2R device. The improvement is attributed to reduced magnetic turbulence.

NNLO computational techniques: The cases H→γγ and H→gg

NASA Astrophysics Data System (ADS)

Actis, Stefano; Passarino, Giampiero; Sturm, Christian; Uccirati, Sandro

2009-04-01

A large set of techniques needed to compute decay rates at the two-loop level are derived and systematized. The main emphasis of the paper is on the two Standard Model decays H→γγ and H→gg. The techniques, however, have a much wider range of application: they give practical examples of general rules for two-loop renormalization; they introduce simple recipes for handling internal unstable particles in two-loop processes; they illustrate simple procedures for the extraction of collinear logarithms from the amplitude. The latter is particularly relevant to show cancellations, e.g. cancellation of collinear divergencies. Furthermore, the paper deals with the proper treatment of non-enhanced two-loop QCD and electroweak contributions to different physical (pseudo-)observables, showing how they can be transformed in a way that allows for a stable numerical integration. Numerical results for the two-loop percentage corrections to H→γγ,gg are presented and discussed. When applied to the process pp→gg+X→H+X, the results show that the electroweak scaling factor for the cross section is between -4% and +6% in the range 100 GeV

Degeneracy relations in QCD and the equivalence of two systematic all-orders methods for setting the renormalization scale

DOE PAGES

Bi, Huan -Yu; Wu, Xing -Gang; Ma, Yang; ...

2015-06-26

The Principle of Maximum Conformality (PMC) eliminates QCD renormalization scale-setting uncertainties using fundamental renormalization group methods. The resulting scale-fixed pQCD predictions are independent of the choice of renormalization scheme and show rapid convergence. The coefficients of the scale-fixed couplings are identical to the corresponding conformal series with zero β-function. Two all-orders methods for systematically implementing the PMC-scale setting procedure for existing high order calculations are discussed in this article. One implementation is based on the PMC-BLM correspondence (PMC-I); the other, more recent, method (PMC-II) uses the R δ-scheme, a systematic generalization of the minimal subtraction renormalization scheme. Both approaches satisfymore » all of the principles of the renormalization group and lead to scale-fixed and scheme-independent predictions at each finite order. In this work, we show that PMC-I and PMC-II scale-setting methods are in practice equivalent to each other. We illustrate this equivalence for the four-loop calculations of the annihilation ratio R e+e– and the Higgs partial width I'(H→bb¯). Both methods lead to the same resummed (‘conformal’) series up to all orders. The small scale differences between the two approaches are reduced as additional renormalization group {β i}-terms in the pQCD expansion are taken into account. In addition, we show that special degeneracy relations, which underly the equivalence of the two PMC approaches and the resulting conformal features of the pQCD series, are in fact general properties of non-Abelian gauge theory.« less

Effective model approach to the dense state of QCD matter

NASA Astrophysics Data System (ADS)

Fukushima, Kenji

2011-12-01

The first-principle approach to the dense state of QCD matter, i.e. the lattice-QCD simulation at finite baryon density, is not under theoretical control for the moment. The effective model study based on QCD symmetries is a practical alternative. However the model parameters that are fixed by hadronic properties in the vacuum may have unknown dependence on the baryon chemical potential. We propose a new prescription to constrain the effective model parameters by the matching condition with the thermal Statistical Model. In the transitional region where thermal quantities blow up in the Statistical Model, deconfined quarks and gluons should smoothly take over the relevant degrees of freedom from hadrons and resonances. We use the Polyakov-loop coupled Nambu-Jona-Lasinio (PNJL) model as an effective description in the quark side and show how the matching condition is satisfied by a simple ansäatz on the Polyakov loop potential. Our results favor a phase diagram with the chiral phase transition located at slightly higher temperature than deconfinement which stays close to the chemical freeze-out points.

Neutral Pion Electroproduction in the Δ Resonance Region

DOE Office of Scientific and Technical Information (OSTI.GOV)

Villano, Anthony

2007-11-01

The electroproduction of baryon resonances at high Q 2 is examined. Analysis focuses on the Δ(1232) resonance via exclusive pseudoscalar meson production of π 0 particles. Differential cross sections are extracted for exclusive π 0 electroproduction. In the central invariant mass (W) region the cross sections are used to extract resonant multipole amplitudes. In particular, the ratio of the electric quadrupole to magnetic dipole amplitudes (E2/M1) will be discussed for the Δ(1232) resonance. The transition to pQCD is discussed in terms of E2/M1 and other multipoles. The helicity amplitude A 3/2 can be used as a baryon helicity conservation meter in this context and will be discussed. The fast shrinking of the resonant contribution in the Δ region is observed at this high momentum transfer. Apart from the observables related to pQCD scaling, the transition form factor Gmore » $$*\\atop{M}$$ is extracted along with the scalar to magnetic dipole ratio C2/M1.« less

EsxB, a secreted protein from Bacillus anthracis forms two distinct helical bundles

DOE PAGES

Fan, Yao; Tan, Kemin; Chhor, Gekleng; ...

2015-07-03

The EsxB protein from Bacillus anthracis belongs to the WXG100 family, a group of proteins secreted by a specialized secretion system. We have determined the crystal structures of recombinant EsxB and discovered that the small protein (~10 kDa), comprised of a helix-loop-helix (HLH) hairpin, is capable of associating into two different helical bundles. The two basic quaternary assemblies of EsxB are an antiparallel (AP) dimer and a rarely observed bisecting U (BU) dimer. This structural duality of EsxB is believed to originate from the heptad repeat sequence diversity of the first helix of its HLH hairpin, which allows for twomore » alternative helix packing. The flexibility of EsxB and the ability to form alternative helical bundles underscore the possibility that this protein can serve as an adaptor in secretion and can form hetero-oligomeric helix bundle(s) with other secreted members of the WXG100 family, such as EsxW. The highly conserved WXG motif is located within the loop of the HLH hairpin and is mostly buried within the helix bundle suggesting that its role is mainly structural. The exact functions of the motif, including a proposed role as a secretion signal, remain unknown.« less

Proof of principle in a de novo designed protein maquette: an allosterically regulated, charge-activated conformational switch in a tetra-alpha-helix bundle.

PubMed

Grosset, A M; Gibney, B R; Rabanal, F; Moser, C C; Dutton, P L

2001-05-08

New understanding of the engineering and allosteric regulation of natural protein conformational switches (such as those that couple chemical and ionic signals, mechanical force, and electro/chemical free energy for biochemical activation, catalysis, and motion) can be derived from simple de novo designed synthetic protein models (maquettes). We demonstrate proof of principle of both reversible switch action and allosteric regulation in a tetra-alpha-helical bundle protein composed of two identical di-helical subunits containing heme coordinated at a specific position close to the disulfide loop region. Individual bundles assume one of two switch states related by large-scale mechanical changes: a syn-topology (helices of the different subunits parallel) or anti-topology (helices antiparallel). Both the spectral properties of a coproporphyrin probe appended to the loop region and the distance-dependent redox interaction between the hemes identify the topologies. Beginning from a syn-topology, introduction of ferric heme in each subunit (either binding or redox change) shifts the topological balance by 25-50-fold (1.9-2.3 kcal/mol) to an anti-dominance. Charge repulsion between the two internal cationic ferric hemes drives the syn- to anti-switch, as demonstrated in two ways. When fixed in the syn-topology, the second ferric heme binding is 25-80-fold (1.9-2.6 kcal/mol) weaker than the first, and adjacent heme redox potentials are split by 80 mV (1.85 kcal/mol), values that energetically match the shift in topological balance. Allosteric and cooperative regulation of the switch by ionic strength exploits the shielded charge interactions between the two hemes and the exposed, cooperative interactions between the coproporphyrin carboxylates.

Long-wave instabilities of two interlaced helical vortices

NASA Astrophysics Data System (ADS)

Quaranta, H. U.; Brynjell-Rahkola, M.; Leweke, T.; Henningson, D. S.

2016-09-01

We present a comparison between experimental observations and theoretical predictions concerning long-wave displacement instabilities of the helical vortices in the wake of a two-bladed rotor. Experiments are performed with a small-scale rotor in a water channel, using a set-up that allows the individual triggering of various instability modes at different azimuthal wave numbers, leading to local or global pairing of successive vortex loops. The initial development of the instability and the measured growth rates are in good agreement with the predictions from linear stability theory, based on an approach where the helical vortex system is represented by filaments. At later times, local pairing develops into large-scale distortions of the vortices, whereas for global pairing the non-linear evolution returns the system almost to its initial geometry.

New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation

PubMed Central

Mustoe, Anthony M.; Bailor, Maximillian H.; Teixeira, Robert M.; Brooks, Charles L.; Al-Hashimi, Hashim M.

2012-01-01

Recent studies have shown that topological constraints encoded at the RNA secondary structure level involving basic steric and stereochemical forces can significantly restrict the orientations sampled by helices across two-way RNA junctions. Here, we formulate these topological constraints in greater quantitative detail and use this topological framework to rationalize long-standing but poorly understood observations regarding the basic behavior of RNA two-way junctions. Notably, we show that the asymmetric nature of the A-form helix and the finite length of a bulge provide a physical basis for the experimentally observed directionality and bulge-length amplitude dependence of bulge induced inter-helical bends. We also find that the topologically allowed space can be modulated by variations in sequence, particularly with the addition of non-canonical GU base pairs at the junction, and, surprisingly, by the length of the 5′ and 3′ helices. A survey of two-way RNA junctions in the protein data bank confirms that junction residues have a strong preference to adopt looped-in, non-canonically base-paired conformations, providing a route for extending our bulge-directed framework to internal loop motifs and implying a simplified link between secondary and tertiary structure. Finally, our results uncover a new simple mechanism for coupling junction-induced topological constraints with tertiary interactions. PMID:21937512

Diagrammatic exponentiation for products of Wilson lines

NASA Astrophysics Data System (ADS)

Mitov, Alexander; Sterman, George; Sung, Ilmo

2010-11-01

We provide a recursive diagrammatic prescription for the exponentiation of gauge theory amplitudes involving products of Wilson lines and loops. This construction generalizes the concept of webs, originally developed for eikonal form factors and cross sections with two eikonal lines, to general soft functions in QCD and related gauge theories. Our coordinate space arguments apply to arbitrary paths for the lines.

Setting the renormalization scale in pQCD: Comparisons of the principle of maximum conformality with the sequential extended Brodsky-Lepage-Mackenzie approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ma, Hong -Hao; Wu, Xing -Gang; Ma, Yang

A key problem in making precise perturbative QCD (pQCD) predictions is how to set the renormalization scale of the running coupling unambiguously at each finite order. The elimination of the uncertainty in setting the renormalization scale in pQCD will greatly increase the precision of collider tests of the Standard Model and the sensitivity to new phenomena. Renormalization group invariance requires that predictions for observables must also be independent on the choice of the renormalization scheme. The well-known Brodsky-Lepage-Mackenzie (BLM) approach cannot be easily extended beyond next-to-next-to-leading order of pQCD. Several suggestions have been proposed to extend the BLM approach tomore » all orders. In this paper we discuss two distinct methods. One is based on the “Principle of Maximum Conformality” (PMC), which provides a systematic all-orders method to eliminate the scale and scheme ambiguities of pQCD. The PMC extends the BLM procedure to all orders using renormalization group methods; as an outcome, it significantly improves the pQCD convergence by eliminating renormalon divergences. An alternative method is the “sequential extended BLM” (seBLM) approach, which has been primarily designed to improve the convergence of pQCD series. The seBLM, as originally proposed, introduces auxiliary fields and follows the pattern of the β0-expansion to fix the renormalization scale. However, the seBLM requires a recomputation of pQCD amplitudes including the auxiliary fields; due to the limited availability of calculations using these auxiliary fields, the seBLM has only been applied to a few processes at low orders. In order to avoid the complications of adding extra fields, we propose a modified version of seBLM which allows us to apply this method to higher orders. As a result, we then perform detailed numerical comparisons of the two alternative scale-setting approaches by investigating their predictions for the annihilation cross section ratio R e+e– at four-loop order in pQCD.« less

Higgs Amplitudes from N=4 Supersymmetric Yang-Mills Theory.

PubMed

Brandhuber, Andreas; Kostacińska, Martyna; Penante, Brenda; Travaglini, Gabriele

2017-10-20

Higgs plus multigluon amplitudes in QCD can be computed in an effective Lagrangian description. In the infinite top-mass limit, an amplitude with a Higgs boson and n gluons is computed by the form factor of the operator TrF^{2}. Up to two loops and for three gluons, its maximally transcendental part is captured entirely by the form factor of the protected stress tensor multiplet operator T_{2} in N=4 supersymmetric Yang-Mills theory. The next order correction involves the calculation of the form factor of the higher-dimensional, trilinear operator TrF^{3}. We present explicit results at two loops for three gluons, including the subleading transcendental terms derived from a particular descendant of the Konishi operator that contains TrF^{3}. These are expressed in terms of a few universal building blocks already identified in earlier calculations. We show that the maximally transcendental part of this quantity, computed in nonsupersymmetric Yang-Mills theory, is identical to the form factor of another protected operator, T_{3}, in the maximally supersymmetric theory. Our results suggest that the maximally transcendental part of Higgs amplitudes in QCD can be entirely computed through N=4 super Yang-Mills theory.

Heavy quark free energy in QCD and in gauge theories with gravity duals

NASA Astrophysics Data System (ADS)

Noronha, Jorge

2010-09-01

Recent lattice results in pure glue SU(3) theory at high temperatures have shown that the expectation value of the renormalized Polyakov loop approaches its asymptotic limit at high temperatures from above. We show that this implies that the “heavy quark free energy” obtained from the renormalized loop computed on the lattice does not behave like a true thermodynamic free energy. While this should be expected to occur in asymptotically free gauge theories such as QCD, we use the gauge/string duality to show that in a large class of strongly coupled gauge theories with nontrivial UV fixed points the Polyakov loop reaches its asymptotic value from above only if the dimension of the relevant operator used to deform the conformal field theory is greater than or equal to 3.

Vector two-point functions in finite volume using partially quenched chiral perturbation theory at two loops

NASA Astrophysics Data System (ADS)

Bijnens, Johan; Relefors, Johan

2017-12-01

We calculate vector-vector correlation functions at two loops using partially quenched chiral perturbation theory including finite volume effects and twisted boundary conditions. We present expressions for the flavor neutral cases and the flavor charged case with equal masses. Using these expressions we give an estimate for the ratio of disconnected to connected contributions for the strange part of the electromagnetic current. We give numerical examples for the effects of partial quenching, finite volume and twisting and suggest the use of different twists to check the size of finite volume effects. The main use of this work is expected to be for lattice QCD calculations of the hadronic vacuum polarization contribution to the muon anomalous magnetic moment.

Topics in Nonsupersymmetric Scattering Amplitudes in Gauge and Gravity Theories

NASA Astrophysics Data System (ADS)

Nohle, Joshua David

In Chapters 1 and 2, we introduce and review the duality between color and kinematics in Yang-Mills theory uncovered by Bern, Carrasco and Johansson (BCJ). In Chapter 3, we provide evidence in favor of the conjectured duality between color and kinematics for the case of nonsupersymmetric pure Yang-Mills amplitudes by constructing a form of the one-loop four-point amplitude of this theory that makes the duality manifest. Our construction is valid in any dimension. We also describe a duality-satisfying representation for the two-loop four-point amplitude with identical four-dimensional external helicities. We use these results to obtain corresponding gravity integrands for a theory containing a graviton, dilaton, and antisymmetric tensor, simply by replacing color factors with specified diagram numerators. Using this, we give explicit forms of ultraviolet divergences at one loop in four, six, and eight dimensions, and at two loops in four dimensions. In Chapter 4, we extend the four-point one-loop nonsupersymmetric pure Yang-Mills discussion of Chapter 3 to include fermions and scalars circulating in the loop with all external gluons. This gives another nontrivial loop-level example showing that the duality between color and kinematics holds in nonsupersymmetric gauge theory. The construction is valid in any spacetime dimension and written in terms of formal polarization vectors. We also convert these expressions into a four-dimensional form with explicit external helicity states. Using this, we compare our results to one-loop duality-satisfying amplitudes that are already present in literature. In Chapter 5, we switch from the topic of color-kinematics duality to discuss the recently renewed interest in the soft behavior of gravitons and gluons. Specifically, we discuss the subleading low-energy behavior. Cachazo and Strominger recently proposed an extension of the soft-graviton theorem found by Weinberg. In addition, they proved the validity of their extension at tree level. This was motivated by a Virasoro symmetry of the gravity S-matrix related to BMS symmetry. As shown long ago by Weinberg, the leading soft behavior is not corrected by loops. In contrast, we show in Chapter 6 that with the standard definition of soft limits in dimensional regularization, the subleading behavior is anomalous and modified by loop effects. We argue that there are no new types of corrections to the first subleading behavior beyond one loop and to the second subleading behavior beyond two loops. To facilitate our investigation, we introduce a new momentum-conservation prescription for defining the subleading terms of the soft limit. We discuss the loop-level subleading soft behavior of gauge-theory amplitudes before turning to gravity amplitudes. In Chapter 7, we show that at tree level, on-shell gauge invariance can be used to fully determine the first subleading soft-gluon behavior and the first two subleading soft-graviton behaviors. Our proofs of the behaviors for n-gluon and n-graviton tree amplitudes are valid in D dimensions and are similar to Low's proof of universality of the first subleading behavior of photons. In contrast to photons coupling to massive particles, in four dimensions the soft behaviors of gluons and gravitons are corrected by loop effects. We comment on how such corrections arise from this perspective. We also show that loop corrections in graviton amplitudes arising from scalar loops appear only at the second soft subleading order. This case is particularly transparent because it is not entangled with graviton infrared singularities. Our result suggests that if we set aside the issue of infrared singularities, soft-graviton Ward identities of extended BMS symmetry are not anomalous through the first subleading order. Finally, in Chapter 8, we conclude this dissertation with a discussion of the evanescent effects on nonsupersymmetric gravity at two loops. Evanescent operators such as the Gauss- Bonnet term have vanishing perturbative matrix elements in exactly D = 4 dimensions. Similarly, evanescent fields do not propagate in D = 4; a three-form field is in this class, since it is dual to a cosmological-constant contribution. In this chapter, we show that evanescent operators and fields modify the leading ultraviolet divergence in pure gravity. To analyze the divergence, we compute the two-loop identical-helicity four-graviton amplitude and determine the coefficient of the associated (non-evanescent) R3 counterterm studied long ago by Goroff and Sagnotti. We compare two pairs of theories that are dual in D = 4: gravity coupled to nothing or to three-form matter, and gravity coupled to zero-form or to two-form matter. Duff and van Nieuwenhuizen showed that, curiously, the one-loop conformal anomaly---the coefficient of the Gauss-Bonnet operator---changes under p-form duality transformations. We concur, and also find that the leading R3 divergence changes under duality transformations. Nevertheless, in both cases the physical renormalized two-loop identical-helicity four-graviton amplitude can be chosen to respect duality. Its renormalization-scale dependence is unaltered. (Abstract shortened by UMI.).

An RNA internal loop acts as a hinge to facilitate ribozyme folding and catalysis.

PubMed Central

Szewczak, A A; Cech, T R

1997-01-01

RNA molecules commonly consist of helical regions separated by internal loops, and in many cases these internal loops have been found to assume stable structures. We have examined the function and dynamics of an internal loop, J5/5a, that joins the two halves of the P4-P6 domain of the Tetrahymena self-splicing group I intron. P4-P6 RNAs with mutations in the J5/5a region showed nondenaturing gel electrophoretic mobilities and levels of Fe(II)-EDTA cleavage protection intermediate between those of wild-type RNA and a mutant incapable of folding into the native P4-P6 tertiary structure. Mutants with the least structured J5/5a loops behaved the most like wild-type P4-P6, and required smaller amounts of Mg2+ to rescue folding. The activity of reconstituted introns containing mutant P4-P6 RNAs correlated similarly with the nature of the J5/5a mutation. Our results suggest that, in solution, the P4-P6 RNA is in a two-state equilibrium between folded and unfolded states. We conclude that this internal loop mainly acts as a flexible hinge, allowing the coaxially stacked helical regions on either side of it to interact via specific tertiary contacts. To a lesser extent, the specific bases within the loop contribute to folding. Furthermore, it is crucial that the junction remain unstructured in the unfolded state. These conclusions cannot be derived from a simple examination of the P4-P6 crystal structure (Cate JH et al., 1996, Science 273:1678-1685), showing once again that structure determination must be supplemented with mutational and thermodynamic analysis to provide a complete picture of a folded macromolecule. PMID:9257643

π Spin Berry Phase in a Quantum-Spin-Hall-Insulator-Based Interferometer: Evidence for the Helical Spin Texture of the Edge States

NASA Astrophysics Data System (ADS)

Chen, Wei; Deng, Wei-Yin; Hou, Jing-Min; Shi, D. N.; Sheng, L.; Xing, D. Y.

2016-08-01

The quantum spin Hall insulator is characterized by helical edge states, with the spin polarization of the electron being locked to its direction of motion. Although the edge-state conduction has been observed, unambiguous evidence of the helical spin texture is still lacking. Here, we investigate the coherent edge-state transport in an interference loop pinched by two point contacts. Because of the helical character, the forward interedge scattering enforces a π spin rotation. Two successive processes can only produce a nontrivial 2 π or trivial 0 spin rotation, which can be controlled by the Rashba spin-orbit coupling. The nontrivial spin rotation results in a geometric π Berry phase, which can be detected by a π phase shift of the conductance oscillation relative to the trivial case. Our results provide smoking gun evidence for the helical spin texture of the edge states. Moreover, it also provides the opportunity to all electrically explore the trajectory-dependent spin Berry phase in condensed matter.

First Plasma Results from the HIT-SI Spheromak

NASA Astrophysics Data System (ADS)

Sieck, P. E.; Hamp, W. T.; Izzo, V. A.; Jarboe, T. R.; Nelson, B. A.; O'Neill, R. G.; Redd, A. J.; Smith, R. J.

2003-10-01

HIT-SI is the newest device in the Helicity Injected Torus (HIT) program. HIT-SI is a ``bow tie'' spheromak formed and sustained by Steady Inductive Helicity Injection (SIHI) current drive. SIHI injects helicity at a nearly constant rate with no open field lines intersecting the boundary. (T. R. Jarboe, Fusion Technology 36) (1), p. 85, 1999 HIT-SI has been designed with a bow tie geometry to achieve stable high-β (>10%) spheromak equilibria. (U. Shumlak and T. R. Jarboe, Phys. Plasmas 7) (7), p. 2959, 2000 Diagnostics currently include surface magnetic probes and flux loops, visible light imaging, H-alpha line radiation monitors, voltage measurements across insulating breaks, injector current Rogowski coils, and injector flux loops. HIT-SI is currently operating in parallel with experiments on HIT-II. At the conclusion of HIT-II operations, HIT-SI will inherit a multi-point Thomson Scattering system, a scanning two-chord FIR interferometer, and other advanced diagnostics, as well as more power supplies to extend the discharge duration. Results are presented which characterize injector operation and possible evidence for spheromak formation.

Cooperative folding of a polytopic α-helical membrane protein involves a compact N-terminal nucleus and nonnative loops

PubMed Central

Paslawski, Wojciech; Lillelund, Ove K.; Kristensen, Julie Veje; Schafer, Nicholas P.; Baker, Rosanna P.; Urban, Sinisa; Otzen, Daniel E.

2015-01-01

Despite the ubiquity of helical membrane proteins in nature and their pharmacological importance, the mechanisms guiding their folding remain unclear. We performed kinetic folding and unfolding experiments on 69 mutants (engineered every 2–3 residues throughout the 178-residue transmembrane domain) of GlpG, a membrane-embedded rhomboid protease from Escherichia coli. The only clustering of significantly positive ϕ-values occurs at the cytosolic termini of transmembrane helices 1 and 2, which we identify as a compact nucleus. The three loops flanking these helices show a preponderance of negative ϕ-values, which are sometimes taken to be indicative of nonnative interactions in the transition state. Mutations in transmembrane helices 3–6 yielded predominantly ϕ-values near zero, indicating that this part of the protein has denatured-state–level structure in the transition state. We propose that loops 1–3 undergo conformational rearrangements to position the folding nucleus correctly, which then drives folding of the rest of the domain. A compact N-terminal nucleus is consistent with the vectorial nature of cotranslational membrane insertion found in vivo. The origin of the interactions in the transition state that lead to a large number of negative ϕ-values remains to be elucidated. PMID:26056273

Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements

PubMed Central

PENEDO, J. CARLOS; WILSON, TIMOTHY J.; JAYASENA, SUMEDHA D.; KHVOROVA, ANASTASIA; LILLEY, DAVID M.J.

2004-01-01

It has been shown that the activity of the hammerhead ribozyme at μM magnesium ion concentrations is markedly increased by the inclusion of loops in helices I and II. We have studied the effect of such loops on the magnesium ion-induced folding of the ribozyme, using fluorescence resonance energy transfer. We find that with the loops in place, folding into the active conformation occurs in a single step, in the μM range of magnesium ion concentration. Disruption of the loop–loop interaction leads to a reversion to two-step folding, with the second stage requiring mM concentrations of magnesium ion. Sodium ions also promote the folding of the natural form of the ribozyme at high concentrations, but the folding occurs as a two-stage process. The loops clearly act as important auxiliary elements in the function of the ribozyme, permitting folding to occur efficiently under physiological conditions. PMID:15100442

Prokaryotic and eukaryotic features observed on the secondary structures of Giardia SSU rRNAs and its phylogenetic implications.

PubMed

Hwang, Ui Wook

2007-04-01

Phylogenetic position of a diplomonad protist Giardia, a principle cause of diarrhea, among eukaryotes has been vigorously debated so far. Through the comparisons of primary and secondary structures of SSU rRNAs of G. intestinalis, G. microti, G. ardeae, and G. muris, I found two major indel regions (a 6-nt indel and a 22-26-nt indel), which correspond to the helix 10 of the V2 region and helices E23-8 to E23-9 of the V4 region, respectively. As generally shown in eukaryotes, G. intestinalis and G. microti have commonly a relatively longer helix 10 (a 7-bp stem and a 4-nt loop), and also the eukaryote-specific helices E23-6 to E23-9. On the other hand, G. muris and G. ardeae have a shorter helix 10: a 2-bp stem and a 6-nt loop in G. ardeae and a 3-bp stem and a 6-nt loop in G. muris. In the V4, they have a single long helix (like the P23-1 helix in prokaryotes) instead of the helices E23-6 to E23-9. Among the four Giardia species, co-appearance of prokaryote- and eukaryote-typical features might be significant evidence to suggest that Giardia (Archezoa) is a living fossil showing an "intermediate stage" during the evolution from prokaryotes to eukaryotes.

Precise MS light-quark masses from lattice QCD in the regularization invariant symmetric momentum-subtraction scheme

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gorbahn, Martin; Jaeger, Sebastian; Department of Physics and Astronomy, University of Sussex, Falmer, Brighton BN1 9QH

2010-12-01

We compute the conversion factors needed to obtain the MS and renormalization-group-invariant (RGI) up, down, and strange quark masses at next-to-next-to-leading order from the corresponding parameters renormalized in the recently proposed RI/SMOM and RI/SMOM{sub {gamma}{sub {mu}} }renormalization schemes. This is important for obtaining the MS masses with the best possible precision from numerical lattice QCD simulations, because the customary RI{sup (')}/MOM scheme is afflicted with large irreducible uncertainties both on the lattice and in perturbation theory. We find that the smallness of the known one-loop matching coefficients is accompanied by even smaller two-loop contributions. From a study of residual scalemore » dependences, we estimate the resulting perturbative uncertainty on the light-quark masses to be about 2% in the RI/SMOM scheme and about 3% in the RI/SMOM{sub {gamma}{sub {mu}} }scheme. Our conversion factors are given in fully analytic form, for general covariant gauge and renormalization point. We provide expressions for the associated anomalous dimensions.« less

MS overline -on-shell quark mass relation up to four loops in QCD and a general SU (N ) gauge group

NASA Astrophysics Data System (ADS)

Marquard, Peter; Smirnov, Alexander V.; Smirnov, Vladimir A.; Steinhauser, Matthias; Wellmann, David

2016-10-01

We compute the relation between heavy quark masses defined in the modified minimal subtraction and the on-shell schemes. Detailed results are presented for all coefficients of the SU (Nc) color factors. The reduction of the four-loop on-shell integrals is performed for a general QCD gauge parameter. Altogether there are about 380 master integrals. Some of them are computed analytically, others with high numerical precision using Mellin-Barnes representations, and the rest numerically with the help of FIESTA. We discuss in detail the precise numerical evaluation of the four-loop master integrals. Updated relations between various short-distance masses and the MS ¯ quark mass to next-to-next-to-next-to-leading order accuracy are provided for the charm, bottom and top quarks. We discuss the dependence on the renormalization and factorization scale.

General structure of fermion two-point function and its spectral representation in a hot magnetized medium

NASA Astrophysics Data System (ADS)

Das, Aritra; Bandyopadhyay, Aritra; Roy, Pradip K.; Mustafa, Munshi G.

2018-02-01

We have systematically constructed the general structure of the fermion self-energy and the effective quark propagator in the presence of a nontrivial background such as a hot magnetized medium. This is applicable to both QED and QCD. The hard thermal loop approximation has been used for the heat bath. We have also examined transformation properties of the effective fermion propagator under some of the discrete symmetries of the system. Using the effective fermion propagator we have analyzed the fermion dispersion spectra in a hot magnetized medium along with the spinor for each fermion mode obtained by solving the modified Dirac equation. The fermion spectra is found to reflect the discrete symmetries of the two-point functions. We note that for a chirally symmetric theory the degenerate left- and right-handed chiral modes in vacuum or in a heat bath get separated and become asymmetric in the presence of a magnetic field without disturbing the chiral invariance. The obtained general structure of the two-point functions is verified by computing the three-point function, which agrees with the existing results in one-loop order. Finally, we have computed explicitly the spectral representation of the two-point functions which would be very important to study the spectral properties of the hot magnetized medium corresponding to QED and QCD with background magnetic field.

Structure of a short-chain dehydrogenase/reductase from Bacillus anthracis

PubMed Central

Hou, Jing; Wojciechowska, Kamila; Zheng, Heping; Chruszcz, Maksymilian; Cooper, David R.; Cymborowski, Marcin; Skarina, Tatiana; Gordon, Elena; Luo, Haibin; Savchenko, Alexei; Minor, Wladek

2012-01-01

The crystal structure of a short-chain dehydrogenase/reductase from Bacillus anthracis strain ‘Ames Ancestor’ complexed with NADP has been determined and refined to 1.87 Å resolution. The structure of the enzyme consists of a Rossmann fold composed of seven parallel β-strands sandwiched by three α-­helices on each side. An NADP molecule from an endogenous source is bound in the conserved binding pocket in the syn conformation. The loop region responsible for binding another substrate forms two perpendicular short helices connected by a sharp turn. PMID:22684058

Transmembrane helix prediction: a comparative evaluation and analysis.

PubMed

Cuthbertson, Jonathan M; Doyle, Declan A; Sansom, Mark S P

2005-06-01

The prediction of transmembrane (TM) helices plays an important role in the study of membrane proteins, given the relatively small number (approximately 0.5% of the PDB) of high-resolution structures for such proteins. We used two datasets (one redundant and one non-redundant) of high-resolution structures of membrane proteins to evaluate and analyse TM helix prediction. The redundant (non-redundant) dataset contains structure of 434 (268) TM helices, from 112 (73) polypeptide chains. Of the 434 helices in the dataset, 20 may be classified as 'half-TM' as they are too short to span a lipid bilayer. We compared 13 TM helix prediction methods, evaluating each method using per segment, per residue and termini scores. Four methods consistently performed well: SPLIT4, TMHMM2, HMMTOP2 and TMAP. However, even the best methods were in error by, on average, about two turns of helix at the TM helix termini. The best and worst case predictions for individual proteins were analysed. In particular, the performance of the various methods and of a consensus prediction method, were compared for a number of proteins (e.g. SecY, ClC, KvAP) containing half-TM helices. The difficulties of predicting half-TM helices suggests that current prediction methods successfully embody the two-state model of membrane protein folding, but do not accommodate a third stage in which, e.g., short helices and re-entrant loops fold within a bundle of stable TM helices.

Electromagnetic corrections to the hadronic vacuum polarization of the photon within QEDL and QEDM

NASA Astrophysics Data System (ADS)

Bussone, Andrea; Della Morte, Michele; Janowski, Tadeusz

2018-03-01

We compute the leading QED corrections to the hadronic vacuum polarization (HVP) of the photon, relevant for the determination of leptonic anomalous magnetic moments, al. We work in the electroquenched approximation and use dynamical QCD configurations generated by the CLS initiative with two degenerate flavors of nonperturbatively O(a)-improved Wilson fermions. We consider QEDL and QEDM to deal with the finite-volume zero modes. We compare results for the Wilson loops with exact analytical determinations. In addition we make sure that the volumes and photon masses used in QEDM are such that the correct dispersion relation is reproduced by the energy levels extracted from the charged pions two-point functions. Finally we compare results for pion masses and the HVP between QEDL and QEDM. For the vacuum polarization, corrections with respect to the pure QCD case, at fixed pion masses, turn out to be at the percent level.

Lattice QCD investigation of the structure of the a0(980 ) meson

NASA Astrophysics Data System (ADS)

Alexandrou, Constantia; Berlin, Joshua; Dalla Brida, Mattia; Finkenrath, Jacob; Leontiou, Theodoros; Wagner, Marc

2018-02-01

We investigate the quark content of the low-lying states in the I (JP)=1 (0+) sector, which are the quantum numbers of the a0(980 ) meson, using lattice QCD. To this end, we consider correlation functions of six different two- and four-quark interpolating fields. We evaluate all diagrams, including diagrams, where quarks propagate within a time slice, e.g. with closed quark loops. We demonstrate that diagrams containing such closed quark loops have a drastic effect on the final results and, thus, may not be neglected. Our analysis, which is carried out at unphysically heavy u and d quark mass corresponding to mπ=296 (3 ) MeV and in a single spatial volume of extent 2.9 fm, shows that in addition to the expected spectrum of two-meson scattering states there is an additional energy level around the two-particle thresholds of K +K ¯ and η +π . This additional state, which is a candidate for the a0(980 ) meson, couples to a quark-antiquark as well as to a diquark-antidiquark interpolating field, indicating that it is a superposition of an ordinary q ¯q and a tetraquark structure. The analysis is performed using AMIAS, a novel statistical method based on the sampling of all possible spectral decompositions of the considered correlation functions, as well as solving standard generalized eigenvalue problems.

Model for the loop voltage of reversed field pinches

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jarboe, T.R.; Alper, B.

1987-04-01

A simple model is presented that uses the concept of helicity balance to predict the toroidal loop voltage of reversed field pinches (RFP's). Data from the RFP's at Culham (Plasma Phys. Controlled Fusion 27, 1307 (1985)) are used to calibrate and verify the model. The model indicates that most of the helicity dissipation occurs in edge regions that are outside the limiters or in regions where field lines contact the walls. The value of this new interpretation to future RFP and spheromak experiments is discussed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ye, Qiaozhen; Krug, Robert M.; Tao, Yizhi Jane

Influenza A viruses pose a serious threat to world public health, particularly the currently circulating avian H5N1 viruses. The influenza viral nucleoprotein forms the protein scaffold of the helical genomic ribonucleoprotein complexes, and has a critical role in viral RNA replication. Here we report a 3.2 Angstrom crystal structure of this nucleoprotein, the overall shape of which resembles a crescent with a head and a body domain, with a protein fold different compared with that of the rhabdovirus nucleoprotein. Oligomerization of the influenza virus nucleoprotein is mediated by a flexible tail loop that is inserted inside a neighboring molecule. Thismore » flexibility in the tail loop enables the nucleoprotein to form loose polymers as well as rigid helices, both of which are important for nucleoprotein functions. Single residue mutations in the tail loop result in the complete loss of nucleoprotein oligomerization. An RNA-binding groove, which is found between the head and body domains at the exterior of the nucleoprotein oligomer, is lined with highly conserved basic residues widely distributed in the primary sequence. The nucleoprotein structure shows that only one of two proposed nuclear localization signals are accessible, and suggests that the body domain of nucleoprotein contains the binding site for the viral polymerase. Our results identify the tail loop binding pocket as a potential target for antiviral development.« less

The decay of Λ _b→ p~K^- in QCD factorization approach

NASA Astrophysics Data System (ADS)

Zhu, Jie; Ke, Hong-Wei; Wei, Zheng-Tao

2016-05-01

With only the tree-level operator, the decay of Λ _b→ pK is predicted to be one order smaller than the experimental data. The QCD penguin effects should be taken into account. In this paper, we explore the one-loop QCD corrections to the decay of Λ _b→ pK within the framework of QCD factorization approach. For the baryon system, the diquark approximation is adopted. The transition hadronic matrix elements between Λ _b and p are calculated in the light-front quark model. The branching ratio of Λ _b→ pK is predicted to be about 4.85× 10^{-6}, which is consistent with experimental data (4.9± 0.9)× 10^{-6}. The CP violation is about 5 % in theory.

Vector-Boson Fusion Higgs Production at Three Loops in QCD.

PubMed

Dreyer, Frédéric A; Karlberg, Alexander

2016-08-12

We calculate the next-to-next-to-next-to-leading-order (N^{3}LO) QCD corrections to inclusive vector-boson fusion Higgs production at proton colliders, in the limit in which there is no color exchange between the hadronic systems associated with the two colliding protons. We also provide differential cross sections for the Higgs transverse momentum and rapidity distributions. We find that the corrections are at the 1‰-2‰ level, well within the scale uncertainty of the next-to-next-to-leading-order calculation. The associated scale uncertainty of the N^{3}LO calculation is typically found to be below the 2‰ level. We also consider theoretical uncertainties due to missing higher order parton distribution functions, and provide an estimate of their importance.

Integrands for QCD rational terms and {N} = {4} SYM from massive CSW rules

NASA Astrophysics Data System (ADS)

Elvang, Henriette; Freedman, Daniel Z.; Kiermaier, Michael

2012-06-01

We use massive CSW rules to derive explicit compact expressions for integrands of rational terms in QCD with any number of external legs. Specifically, we present all- n integrands for the one-loop all-plus and one-minus gluon amplitudes in QCD. We extract the finite part of spurious external-bubble contributions systematically; this is crucial for the application of integrand-level CSW rules in theories without supersymmetry. Our approach yields integrands that are independent of the choice of CSW reference spinor even before integration. Furthermore, we present a recursive derivation of the recently proposed massive CSW-style vertex expansion for massive tree amplitudes and loop integrands on the Coulomb-branch of {N} = {4} SYM. The derivation requires a careful study of boundary terms in all-line shift recursion relations, and provides a rigorous (albeit indirect) proof of the recently proposed construction of massive amplitudes from soft-limits of massless on-shell amplitudes. We show that the massive vertex expansion manifestly preserves all holomorphic and half of the anti-holomorphic supercharges, diagram-by-diagram, even off-shell.

Two-loop matching factors for light quark masses and three-loop mass anomalous dimensions in the regularization invariant symmetric momentum-subtraction schemes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Almeida, Leandro G.; Physics Department, Brookhaven National Laboratory, Upton, New York 11973; Sturm, Christian

2010-09-01

Light quark masses can be determined through lattice simulations in regularization invariant momentum-subtraction (RI/MOM) schemes. Subsequently, matching factors, computed in continuum perturbation theory, are used in order to convert these quark masses from a RI/MOM scheme to the MS scheme. We calculate the two-loop corrections in QCD to these matching factors as well as the three-loop mass anomalous dimensions for the RI/SMOM and RI/SMOM{sub {gamma}{sub {mu}} }schemes. These two schemes are characterized by a symmetric subtraction point. Providing the conversion factors in the two different schemes allows for a better understanding of the systematic uncertainties. The two-loop expansion coefficients ofmore » the matching factors for both schemes turn out to be small compared to the traditional RI/MOM schemes. For n{sub f}=3 quark flavors they are about 0.6%-0.7% and 2%, respectively, of the leading order result at scales of about 2 GeV. Therefore, they will allow for a significant reduction of the systematic uncertainty of light quark mass determinations obtained through this approach. The determination of these matching factors requires the computation of amputated Green's functions with the insertions of quark bilinear operators. As a by-product of our calculation we also provide the corresponding results for the tensor operator.« less

Two-loop matching factors for light quark masses and three-loop mass anomalous dimensions in the RI/SMOM schemes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sturm, C.; Almeida, L.

2010-04-26

Light quark masses can be determined through lattice simulations in regularization invariant momentum-subtraction (RI/MOM) schemes. Subsequently, matching factors, computed in continuum perturbation theory, are used in order to convert these quark masses from a RI/MOM scheme to the {ovr MS} scheme. We calculate the two-loop corrections in QCD to these matching factors as well as the three-loop mass anomalous dimensions for the RI/SMOM and RI/SMOM{sub {gamma}{mu}} schemes. These two schemes are characterized by a symmetric subtraction point. Providing the conversion factors in the two different schemes allows for a better understanding of the systematic uncertainties. The two-loop expansion coefficients ofmore » the matching factors for both schemes turn out to be small compared to the traditional RI/MOM schemes. For n{sub f} = 3 quark flavors they are about 0.6%-0.7% and 2%, respectively, of the leading order result at scales of about 2 GeV. Therefore, they will allow for a significant reduction of the systematic uncertainty of light quark mass determinations obtained through this approach. The determination of these matching factors requires the computation of amputated Green's functions with the insertions of quark bilinear operators. As a by-product of our calculation we also provide the corresponding results for the tensor operator.« less

Scalar correlator at [symbol: see text](alpha(s)4), Higgs boson decay into bottom quarks, and bounds on the light-quark masses.

PubMed

Baikov, P A; Chetyrkin, K G; Kühn, J H

2006-01-13

We compute, for the first time, the absorptive part of the massless correlator of two quark scalar currents in five loops. As physical applications, we consider the [symbol: see text](alpha(s)4) corrections to the decay rate of the standard model Higgs boson into quarks, as well as the constraints on the strange quark mass following from QCD sum rules.

mr: A C++ library for the matching and running of the Standard Model parameters

NASA Astrophysics Data System (ADS)

Kniehl, Bernd A.; Pikelner, Andrey F.; Veretin, Oleg L.

2016-09-01

We present the C++ program library mr that allows us to reliably calculate the values of the running parameters in the Standard Model at high energy scales. The initial conditions are obtained by relating the running parameters in the MS bar renormalization scheme to observables at lower energies with full two-loop precision. The evolution is then performed in accordance with the renormalization group equations with full three-loop precision. Pure QCD corrections to the matching and running are included through four loops. We also provide a Mathematica interface for this program library. Catalogue identifier: AFAI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AFAI_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 517613 No. of bytes in distributed program, including test data, etc.: 2358729 Distribution format: tar.gz Programming language: C++. Computer: IBM PC. Operating system: Linux, Mac OS X. RAM: 1 GB Classification: 11.1. External routines: TSIL [1], OdeInt [2], boost [3] Nature of problem: The running parameters of the Standard Model renormalized in the MS bar scheme at some high renormalization scale, which is chosen by the user, are evaluated in perturbation theory as precisely as possible in two steps. First, the initial conditions at the electroweak energy scale are evaluated from the Fermi constant GF and the pole masses of the W, Z, and Higgs bosons and the bottom and top quarks including the full two-loop threshold corrections. Second, the evolution to the high energy scale is performed by numerically solving the renormalization group evolution equations through three loops. Pure QCD corrections to the matching and running are included through four loops. Solution method: Numerical integration of analytic expressions Additional comments: Available for download from URL: http://apik.github.io/mr/. The MathLink interface is tested to work with Mathematica 7-9 and, with an additional flag, also with Mathematica 10 under Linux and with Mathematica 10 under Mac OS X. Running time: less than 1 second References: [1] S. P. Martin and D. G. Robertson, Comput. Phys. Commun. 174 (2006) 133-151 [hep-ph/0501132]. [2] K. Ahnert and M. Mulansky, AIP Conf. Proc. 1389 (2011) 1586-1589 [arxiv:1110.3397 [cs.MS

Noncommutative QED+QCD and the {beta} function for QED

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ettefaghi, M. M.; Haghighat, M.; Mohammadi, R.

2010-11-15

QED based on {theta}-unexpanded noncomutative space-time in contrast with the noncommutative QED based on {theta}-expanded U(1) gauge theory via the Seiberg-Witten map is one-loop renormalizable. Meanwhile it suffers from asymptotic freedom that is not in agreement with the experiment. We show that the QED part of the U{sub *}(3)xU{sub *}(1) gauge group as an appropriate gauge group for the noncommutative QED+QCD is not only one-loop renormalizable but also has a {beta} function that can be positive, negative and even zero. In fact the {beta} function depends on the mixing parameter {delta}{sub 13} as a free parameter and it will bemore » equal to its counterpart in the ordinary QED for {delta}{sub 13}=0.367{pi}.« less

Dissociation of heavy quarkonium in hot QCD medium in a quasiparticle model

NASA Astrophysics Data System (ADS)

Agotiya, Vineet Kumar; Chandra, Vinod; Jamal, M. Yousuf; Nilima, Indrani

2016-11-01

Following a recent work on the effective description of the equations of state for hot QCD obtained from a hard thermal loop expression for the gluon self-energy, in terms of the quasigluons and quasiquarks and antiquarks with respective effective fugacities, the dissociation process of heavy quarkonium in hot QCD medium has been investigated. This has been done by investigating the medium modification to a heavy quark potential. The medium-modified potential has a quite different form (a long-range Coulomb tail in addition to the usual Yukawa term) in contrast to the usual picture of Debye screening. The flavor dependence binding energies of the heavy quarkonia states and the dissociation temperature have been obtained by employing the Debye mass for pure gluonic and full QCD case computed employing the quasiparticle picture. Thus, estimated dissociation patterns of the charmonium and bottomonium states, considering Debye mass from different approaches in the pure gluonic case and full QCD, have shown good agreement with the other potential model studies.

Structural effects of extracellular loop mutations in CFTR helical hairpins.

PubMed

Chang, Yuan-Heng; Stone, Tracy A; Chin, Stephanie; Glibowicka, Mira; Bear, Christine E; Deber, Charles M

2018-05-01

Missense mutations constitute 40% of 2000 cystic fibrosis-phenotypic mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) database, yet the precise mechanism as to how a point mutation can render the entire 1480-residue CFTR protein dysfunctional is not well-understood. Here we investigate the structural effects of two CF-phenotypic mutations - glutamic acid to glycine at position 217 (E217G) and glutamine to arginine at position 220 (Q220R) - in the extracellular (ECL2) loop region of human CFTR using helical hairpin constructs derived from transmembrane (TM) helices 3 and 4 of the first membrane domain. We systematically replaced the wild type (WT) residues E217 and Q220 with the subset of missense mutations that could arise through a single nucleotide change in their respective codons. Circular dichroism spectra of E217G revealed that a significant increase in helicity vs. WT arises in the membrane-mimetic environment of sodium dodecylsulfate (SDS) micelles, while this mutant showed a similar gel shift to WT on SDS-PAGE gels. In contrast, the CF-mutant Q220R showed similar helicity but an increased gel shift vs. WT. These structural variations are compared with the maturation levels of the corresponding mutant full-length CFTRs, which we found are reduced to approx. 50% for E217G and 30% for Q220R vs. WT. The overall results with CFTR hairpins illustrate the range of impacts that single mutations can evoke in intramolecular protein-protein and/or protein-lipid interactions - and the levels to which corresponding mutations in full-length CFTR may be flagged by quality control mechanisms during biosynthesis. Copyright © 2018 Elsevier B.V. All rights reserved.

Polarization components in π 0 photoproduction at photon energies up to 5.6 GeV

DOE PAGES

Luo, W.; Brash, E. J.; Gilman, R.; ...

2012-05-31

We present new data for the polarization observables of the final state proton in the 1H(→ γ, → p)π 0 reaction. These data can be used to test predictions based on hadron helicity conservation (HHC) and perturbative QCD (pQCD). These data have both small statistical and systematic uncertainties, and were obtained with beam energies between 1.8 and 5.6 GeV and for π 0 scattering angles larger than 75{sup o} in center-of-mass (c.m.) frame. The data extend the polarization measurements data base for neutral pion photoproduction up to E γ = 5.6 GeV. The results show non-zero induced polarization above themore » resonance region. The polarization transfer components vary rapidly with the photon energy and π 0 scattering angle in the center-of-mass frame. This indicates that HHC does not hold and that the pQCD limit is still not reached in the energy regime of this experiment.« less

Direct Evaluation of the Quark Content of Nucleons from Lattice QCD at the Physical Point.

PubMed

Abdel-Rehim, A; Alexandrou, C; Constantinou, M; Hadjiyiannakou, K; Jansen, K; Kallidonis, Ch; Koutsou, G; Avilés-Casco, A Vaquero

2016-06-24

We evaluate the light, strange, and charm scalar content of the nucleon using one lattice QCD ensemble generated with two degenerate light quarks with mass fixed to their physical value. We use improved techniques to evaluate the disconnected quark loops to sufficient accuracy to determine the strange and charm nucleon σ terms in addition to the light quark content σ_{πN}. We find σ_{πN}=37.2(2.6)(4.7/2.9)  MeV, σ_{s}=41.1(8.2)(7.8/5.8)  MeV, and σ_{c}=79(21)(12/8)  MeV, where the first error is statistical and the second is the systematic error due to the determination of the lattice spacing, the assessment of finite volume, and residual excited state effects.

Strong and Electroweak Matter 2004

NASA Astrophysics Data System (ADS)

Eskola, Kari J.; Kainulainen, Kimmo; Kajantie, Keijo; Rummukainen, Kari

RHIC experimental summary: the message from pp, d+Au and Au+Au collisions / M. Calderón de la Barca Sánchez -- Hydrodynamic aspects of relativistic heavy ion collisions at RHIC / P. F. Kolb -- Photon emission in a hot QCD plasma / P. Aurenche -- In search of the saturation scale: intrinsic features of the CGC / H. Weigert -- From leading hadron suppression to jet quenching at RHIC and LHC / U. A. Wiedemann -- Lattice simulations with chemical potential / C. Schmidt -- Mesonic correlators in hot QCD / M. Laine -- Thermalization and plasma instabilities / P. Arnold -- Transport coefficients in hot QCD / G. D. Moore -- Classical fields and heavy ion collisions / T. Lappi -- Progress in nonequilibrium quantum field theory II / J. Berges and J. Serreau -- A general effective theory for dense quark matter / P. T. Reuter, Q. Wang and D. H. Rischke -- Thermal leptogenesis / M. Plümacher -- Cold electroweak Baryogenesis / J. Smit -- Proton-nucleus collisions in the color glass condensate framework / J.-P. Blaizot, F. Gelis and R. Venugopalan -- From classical to quantum saturation in the nuclear wavefunction / D. N. Triantafyllopoulos -- Charge correlations in heavy ion collisions / A. Rajantie -- Whitening of the quark-gluon plasma / S. Mrówczyński -- Progress in anisotropic plasma physics / P. Romatschke and M. Strickland -- Deconfinement and chiral symmetry: competing orders / K. Tuominen -- Relation between the chiral and deconfinement phase transitions / Y. Hatta -- Renormalized Polyakov loops, matrix models and the Gross-Witten point / A. Dumitru and J. T. Lenaghan -- The nature of the soft excitation at the critical end point of QCD / A. Jakovác ... [et al.] -- Thermodynamics of the 1+1-dimensional nonlinear sigma model through next-to-leading order in 1/N / H. J. Warringa -- Light quark meson correlations at high temperature / E. Laemann ... [et al.] -- Charmonia at finite momenta in a deconfined plasma / S. Datta ... [et al.] -- QCD thermodynamics: lattice results confront models / M. D'Elia and M. P. Lombardo -- Singlet free energies of a static quark-antiquark pair / K. Petrov -- Contributions to transport theory from multi-particle interactions and production processes / M. E. Carrington -- Transport coefficients and the 2PI effective action in the large N limit / G. Aarts and J. M. Martinez Resco -- Thermal features far from equilibrium: prethermalization / S. Borsányi -- QCD phase diagram at small Baryon densities from imaginary [symbol]: status report / O. Philipsen and Ph. de Forcrand -- Two loop renormalisation of the magnetic coupling in hot QCD and spatial Wilson loop / P. Giovannangeli -- Thermodynamics of deconfined QCD at small and large chemical potential / A. Ipp -- Evading the infrared problem of thermal QCD / Y. Schroder -- Chiral mesons in hot matter / A. Gómez Nicola, F. J. Llanes-Estrada and J. R. Peláez -- Thermal production of axinos in the early universe / A. Brandenburg and F. D. Steffen -- The 2-PI-1/N approximation applied to tachyonic preheating / A. Tranberg, A. Arrizabalaga and J. Smit -- Nonequilibrium dynamics in scalar hybrid models / J. Baacke and A. Heinen -- Photon mass in inflation and nearly minimal magnetogenesis / T. Prokopec -- Transport equations for chiral fermions to order [symbol] and electroweak Baryogenesis / S. Weinstock, M. G. Schmidt and T. Prokopec -- The gapless 2SC phase / M. Huang and I. A. Shovkovy -- Gapless CFL and its competition with mixed phases / M. Alford, C. Kouvaris and K. Rajagopal -- Transport coefficients in color superconducting quark matter / C. Manuel -- Renormalization and resummation in finite temperature field theories / A. Jakovác and Zs. Szép -- Renormalization and gauge symmetry for 2PI effective actions / U. Reinosa -- Out-of-equilibrium massless Schwinger model / R. F. Alvarez-Estrada -- Selfconsistent calculations of hadrons at finite temperature / C. Beckmann -- Fermion production in classical fields / D. D. Dietrich -- Numerical study of the equation of state for two flavor QCD at non-zero Baryon density / S. Ejiri ... [et al.] -- Phase conversion after a chiral transition: effects from inhomogeneities and finite size / E. S. Fraga -- Coherent Baryogenesis and nonthermal leptogenesis: a comparison / B. Garbrecht, T. Prokopec and M. G. Schmidt -- Two aspects of color superconductivity: gauge independence and neutrality / A. Gerhold -- QCD phase diagram in nonlocal chiral quark models / D. Gómez Dumm -- QCD equation of state and dark matter / M. Hindmarsh and O. Philipsen -- Analytical approach to SU(2) Yang-Mills thermodynamics / R. Hofmann -- Free energies of static three quark systems / K. Hübner ... [et al.] -- Color ferromagnetic state of dense quark matter / A. Iwazaki -- Axial currents from CKM matrix CP violation and electroweak Baryogenesis / T. Konstandin -- Dilute monopole gas, and K-tensions in gluodynamics / C. P. Korthals Altes and P. Giovannangeli -- Infrared QCD and the renormalisation group / D. F. Litim ... [et al.] -- Residual confinement in high-temperature Yang-Mills theory / A. Maas ... [et al.] -- Scalar O(N) model at finite temperature - 2PI effective potential in different approximations / J. Baacke and S. Michalski -- Cutoff effects in meson spectral functions / T. Blum and P. Petreczky -- Anomalous specific heat in ultradegenerate QED and QCD / A. Gerhold, A. Ipp and A. Rebhan -- Color-superconducting phases in cold and dense quark matter / A. Schmitt -- Non fermi liquid effects in dense matter and compact star cooling / K. Schwenzer and T. Schäfer -- Prethermalisation and the build-up of the Higgs effect / D. Sexty and A. Patkós -- Vector meson at non-zero Baryon density and zero sound / S. J. Hands and C. G. Strouthos -- Impact of Baryon resonances on the chiral phase transition / D. Zschiesche ... [et al.].

On the impact of power corrections in the prediction of B → K *μ+μ- observables

NASA Astrophysics Data System (ADS)

Descotes-Genon, Sébastien; Hofer, Lars; Matias, Joaquim; Virto, Javier

2014-12-01

The recent LHCb angular analysis of the exclusive decay B → K * μ + μ - has indicated significant deviations from the Standard Model expectations. Accurate predictions can be achieved at large K *-meson recoil for an optimised set of observables designed to have no sensitivity to hadronic input in the heavy-quark limit at leading order in α s . However, hadronic uncertainties reappear through non-perturbative ΛQCD /m b power corrections, which must be assessed precisely. In the framework of QCD factorisation we present a systematic method to include factorisable power corrections and point out that their impact on angular observables depends on the scheme chosen to define the soft form factors. Associated uncertainties are found to be under control, contrary to earlier claims in the literature. We also discuss the impact of possible non-factorisable power corrections, including an estimate of charm-loop effects. We provide results for angular observables at large recoil for two different sets of inputs for the form factors, spelling out the different sources of theoretical uncertainties. Finally, we comment on a recent proposal to explain the anomaly in B → K * μ + μ - observables through charm-resonance effects, and we propose strategies to test this proposal identifying observables and kinematic regions where either the charm-loop model can be disentangled from New Physics effects or the two options leave different imprints.

Cutting Edge: Molecular Structure of the IL-1R-Associated Kinase-4 Death Domain and Its Implications for TLR Signaling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lasker, Michael V.; Gajjar, Mark M.; Nair, Satish K.

2010-07-19

IL-1R-associated kinase (IRAK) 4 is an essential component of innate immunity. IRAK-4 deficiency in mice and humans results in severe impairment of IL-1 and TLR signaling. We have solved the crystal structure for the death domain of Mus musculus IRAK-4 to 1.7 {angstrom} resolution. This is the first glimpse of the structural details of a mammalian IRAK family member. The crystal structure reveals a six-helical bundle with a prominent loop, which among IRAKs and Pelle, a Drosophila homologue, is unique to IRAK-4. This highly structured loop contained between helices two and three, comprises an 11-aa stretch. Although innate immune domainmore » recognition is thought to be very similar between Drosophila and mammals, this structural component points to a drastic difference. This structure can be used as a framework for future mutation and deletion studies and potential drug design.« less

Effects of magnesium ions on the stabilization of RNA oligomers of defined structures.

PubMed Central

Serra, Martin J; Baird, John D; Dale, Taraka; Fey, Bridget L; Retatagos, Kimberly; Westhof, Eric

2002-01-01

Optical melting was used to determine the stabilities of 11 small RNA oligomers of defined secondary structure as a function of magnesium ion concentration. The oligomers included helices composed of Watson-Crick base pairs, GA tandem base pairs, GU tandem base pairs, and loop E motifs (both eubacterial and eukaryotic). The effect of magnesium ion concentration on stability was interpreted in terms of two simple models. The first assumes an uptake of metal ion upon duplex formation. The second assumes nonspecific electrostatic attraction of metal ions to the RNA oligomer. For all oligomers, except the eubacterial loop E, the data could best be interpreted as nonspecific binding of metal ions to the RNAs. The effect of magnesium ions on the stability of the eubacterial loop E was distinct from that seen with the other oligomers in two ways. First, the extent of stabilization by magnesium ions (as measured by either change in melting temperature or free energy) was three times greater than that observed for the other helical oligomers. Second, the presence of magnesium ions produces a doubling of the enthalpy for the melting transition. These results indicate that magnesium ion stabilizes the eubacterial loop E sequence by chelating the RNA specifically. Further, these results on a rather small system shed light on the large enthalpy changes observed upon thermal unfolding of large RNAs like group I introns. It is suggested that parts of those large enthalpy changes observed in the folding of RNAs may be assigned to variations in the hydration states and types of coordinating atoms in some specifically bound magnesium ions and to an increase in the observed cooperativity of the folding transition due to the binding of those magnesium ions coupling the two stems together. Brownian dynamic simulations, carried out to visualize the metal ion binding sites, reveal rather delocalized ionic densities in all oligomers, except for the eubacterial loop E, in which precisely located ion densities were previously calculated. PMID:12003491

Hard quark-quark scattering with exclusive reactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barton, D.S.; Bunce, G.M.; Carroll, A.S.

1984-01-01

We present data from ..pi../sup -/p ..-->.. elastic and rho/sup -/p final states for scattering at 90/sup 0/ center of mass, -t = 9 GeV/sup 2//c/sup 2/. A large rho/sup -/p signal is seen and the rho/sup -/ is strongly polarized. This polarization tests a QCD prediction that quarks cannot flip helicity. The test fails dramatically. 9 references, 4 figures.

Helical unwinding and side-chain unlocking unravel the outward open conformation of the melibiose transporter

NASA Astrophysics Data System (ADS)

Wang, Li-Ying; Ravi, Vidhya M.; Leblanc, Gérard; Padrós, Esteve; Cladera, Josep; Perálvarez-Marín, Alex

2016-09-01

Molecular dynamics simulations have been used to study the alternate access mechanism of the melibiose transporter from Escherichia coli. Starting from the outward-facing partially occluded form, 2 out of 12 simulations produced an outward full open form and one partially open, whereas the rest yielded fully or partially occluded forms. The shape of the outward-open form resembles other outward-open conformations of secondary transporters. During the transporter opening, conformational changes in some loops are followed by changes in the periplasm region of transmembrane helix 7. Helical curvature relaxation and unlocking of hydrophobic and ionic locks promote the outward opening of the transporter making accessible the substrate binding site. In particular, FRET studies on mutants of conserved aromatic residues of extracellular loop 4 showed lack of substrate binding, emphasizing the importance of this loop for making crucial interactions that control the opening of the periplasmic side. This study indicates that the alternate access mechanism for the melibiose transporter fits better into a flexible gating mechanism rather than the archetypical helical rigid-body rocker-switch mechanism.

Methods of Contemporary Gauge Theory

NASA Astrophysics Data System (ADS)

Makeenko, Yuri

2002-08-01

Preface; Part I. Path Integrals: 1. Operator calculus; 2. Second quantization; 3. Quantum anomalies from path integral; 4. Instantons in quantum mechanics; Part II. Lattice Gauge Theories: 5. Observables in gauge theories; 6. Gauge fields on a lattice; 7. Lattice methods; 8. Fermions on a lattice; 9. Finite temperatures; Part III. 1/N Expansion: 10. O(N) vector models; 11. Multicolor QCD; 12. QCD in loop space; 13. Matrix models; Part IV. Reduced Models: 14. Eguchi-Kawai model; 15. Twisted reduced models; 16. Non-commutative gauge theories.

Methods of Contemporary Gauge Theory

NASA Astrophysics Data System (ADS)

Makeenko, Yuri

2005-11-01

Preface; Part I. Path Integrals: 1. Operator calculus; 2. Second quantization; 3. Quantum anomalies from path integral; 4. Instantons in quantum mechanics; Part II. Lattice Gauge Theories: 5. Observables in gauge theories; 6. Gauge fields on a lattice; 7. Lattice methods; 8. Fermions on a lattice; 9. Finite temperatures; Part III. 1/N Expansion: 10. O(N) vector models; 11. Multicolor QCD; 12. QCD in loop space; 13. Matrix models; Part IV. Reduced Models: 14. Eguchi-Kawai model; 15. Twisted reduced models; 16. Non-commutative gauge theories.

Complete NLO corrections to W+W+ scattering and its irreducible background at the LHC

NASA Astrophysics Data System (ADS)

Biedermann, Benedikt; Denner, Ansgar; Pellen, Mathieu

2017-10-01

The process pp → μ +ν μ e+νejj receives several contributions of different orders in the strong and electroweak coupling constants. Using appropriate event selections, this process is dominated by vector-boson scattering (VBS) and has recently been measured at the LHC. It is thus of prime importance to estimate precisely each contribution. In this article we compute for the first time the full NLO QCD and electroweak corrections to VBS and its irreducible background processes with realistic experimental cuts. We do not rely on approximations but use complete amplitudes involving two different orders at tree level and three different orders at one-loop level. Since we take into account all interferences, at NLO level the corrections to the VBS process and to the QCD-induced irreducible background process contribute at the same orders. Hence the two processes cannot be unambiguously distinguished, and all contributions to the μ +ν μ e+νejj final state should be preferably measured together.

A subtraction scheme for computing QCD jet cross sections at NNLO: integrating the subtraction terms I

NASA Astrophysics Data System (ADS)

Somogyi, Gábor; Trócsányi, Zoltán

2008-08-01

In previous articles we outlined a subtraction scheme for regularizing doubly-real emission and real-virtual emission in next-to-next-to-leading order (NNLO) calculations of jet cross sections in electron-positron annihilation. In order to find the NNLO correction these subtraction terms have to be integrated over the factorized unresolved phase space and combined with the two-loop corrections. In this paper we perform the integration of all one-parton unresolved subtraction terms.

Diagrammatic representation of scalar QCD and sign problem at nonzero chemical potential

NASA Astrophysics Data System (ADS)

Bruckmann, Falk; Wellnhofer, Jacob

2018-01-01

We consider QCD at strong coupling with scalar quarks coupled to a chemical potential. Performing the link integrals we present a diagrammatic representation of the path integral weight. It is based on mesonic and baryonic building blocks, in close analogy to fermionic QCD. Likewise, the baryon loops are subject to a manifest conservation of the baryon number. The sign problem is expected to disappear in this representation and we do confirm this for three flavors, where a scalar baryon can be built and, thus, a dependence on the chemical potential occurs. For higher flavor number, we analyze examples for a potential sign problem in the baryon sector and conjecture that all weights are positive upon exploring the current conservation of each flavor.

Static quark-antiquark potential in the quark-gluon plasma from lattice QCD.

PubMed

Burnier, Yannis; Kaczmarek, Olaf; Rothkopf, Alexander

2015-02-27

We present a state-of-the-art determination of the complex valued static quark-antiquark potential at phenomenologically relevant temperatures around the deconfinement phase transition. Its values are obtained from nonperturbative lattice QCD simulations using spectral functions extracted via a novel Bayesian inference prescription. We find that the real part, both in a gluonic medium, as well as in realistic QCD with light u, d, and s quarks, lies close to the color singlet free energies in Coulomb gauge and shows Debye screening above the (pseudo)critical temperature T_{c}. The imaginary part is estimated in the gluonic medium, where we find that it is of the same order of magnitude as in hard-thermal loop resummed perturbation theory in the deconfined phase.

Internal loop/bulge and hairpin loop of the iron-responsive element of ferritin mRNA contribute to maximal iron regulatory protein 2 binding and translational regulation in the iso-iron-responsive element/iso-iron regulatory protein family.

PubMed

Ke, Y; Sierzputowska-Gracz, H; Gdaniec, Z; Theil, E C

2000-05-23

Iron-responsive elements (IREs), a natural group of mRNA-specific sequences, bind iron regulatory proteins (IRPs) differentially and fold into hairpins [with a hexaloop (HL) CAGUGX] with helical distortions: an internal loop/bulge (IL/B) (UGC/C) or C-bulge. C-bulge iso-IREs bind IRP2 more poorly, as oligomers (n = 28-30), and have a weaker signal response in vivo. Two trans-loop GC base pairs occur in the ferritin IRE (IL/B and HL) but only one in C-bulge iso-IREs (HL); metal ions and protons perturb the IL/B [Gdaniec et al. (1998) Biochemistry 37, 1505-1512]. IRE function (translation) and physical properties (T(m) and accessibility to nucleases) are now compared for IL/B and C-bulge IREs and for HL mutants. Conversion of the IL/B into a C-bulge by a single deletion in the IL/B or by substituting the HL CG base pair with UA both derepressed ferritin synthesis 4-fold in rabbit reticulocyte lysates (IRP1 + IRP2), confirming differences in IRP2 binding observed for the oligomers. Since the engineered C-bulge IRE was more helical near the IL/B [Cu(phen)(2) resistant] and more stable (T(m) increased) and the HL mutant was less helical near the IL/B (ribonuclease T1 sensitive) and less stable (T(m) decreased), both CG trans-loop base pairs contribute to maximum IRP2 binding and translational regulation. The (1)H NMR spectrum of the Mg-IRE complex revealed, in contrast to the localized IL/B effects of Co(III) hexaammine observed previously, perturbation of the IL/B plus HL and interloop helix. The lower stability and greater helix distortion in the ferritin IL/B-IRE compared to the C-bulge iso-IREs create a combinatorial set of RNA/protein interactions that control protein synthesis rates with a range of signal sensitivities.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fan, Yao; Tan, Kemin; Chhor, Gekleng

The EsxB protein from Bacillus anthracis belongs to the WXG100 family, a group of proteins secreted by a specialized secretion system. We have determined the crystal structures of recombinant EsxB and discovered that the small protein (~10 kDa), comprised of a helix-loop-helix (HLH) hairpin, is capable of associating into two different helical bundles. The two basic quaternary assemblies of EsxB are an antiparallel (AP) dimer and a rarely observed bisecting U (BU) dimer. This structural duality of EsxB is believed to originate from the heptad repeat sequence diversity of the first helix of its HLH hairpin, which allows for twomore » alternative helix packing. The flexibility of EsxB and the ability to form alternative helical bundles underscore the possibility that this protein can serve as an adaptor in secretion and can form hetero-oligomeric helix bundle(s) with other secreted members of the WXG100 family, such as EsxW. The highly conserved WXG motif is located within the loop of the HLH hairpin and is mostly buried within the helix bundle suggesting that its role is mainly structural. The exact functions of the motif, including a proposed role as a secretion signal, remain unknown.« less

Next-to-leading order QCD predictions for top-quark pair production with up to three jets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Höche, S.; Maierhöfer, P.; Moretti, N.

2017-03-07

Here, we present theoretical predictions for the production of top-quark pairs with up to three jets at the next-to leading order in perturbative QCD. The relevant calculations are performed with Sherpa and OpenLoops. In order to address the issue of scale choices and related uncertainties in the presence of multiple scales, we compare results obtained with the standard scale HT/2HT/2 at fixed order and the MiNLO procedure. By analyzing various cross sections and distributions for tmore » $$\\bar{t}$$+0,1,2,3 jets at the 13 TeV LHC we found a remarkable overall agreement between fixed-order and MiNLO results. The differences are typically below the respective factor-two scale variations, suggesting that for all considered jet multiplicities missing higher-order effects should not exceed the ten percent level.« less

Higgs boson decay into b-quarks at NNLO accuracy

NASA Astrophysics Data System (ADS)

Del Duca, Vittorio; Duhr, Claude; Somogyi, Gábor; Tramontano, Francesco; Trócsányi, Zoltán

2015-04-01

We compute the fully differential decay rate of the Standard Model Higgs boson into b-quarks at next-to-next-to-leading order (NNLO) accuracy in αs. We employ a general subtraction scheme developed for the calculation of higher order perturbative corrections to QCD jet cross sections, which is based on the universal infrared factorization properties of QCD squared matrix elements. We show that the subtractions render the various contributions to the NNLO correction finite. In particular, we demonstrate analytically that the sum of integrated subtraction terms correctly reproduces the infrared poles of the two-loop double virtual contribution to this process. We present illustrative differential distributions obtained by implementing the method in a parton level Monte Carlo program. The basic ingredients of our subtraction scheme, used here for the first time to compute a physical observable, are universal and can be employed for the computation of more involved processes.

C -parameter distribution at N 3 LL ' including power corrections

DOE PAGES

Hoang, André H.; Kolodrubetz, Daniel W.; Mateu, Vicent; ...

2015-05-15

We compute the e⁺e⁻ C-parameter distribution using the soft-collinear effective theory with a resummation to next-to-next-to-next-to-leading-log prime accuracy of the most singular partonic terms. This includes the known fixed-order QCD results up to O(α 3 s), a numerical determination of the two-loop nonlogarithmic term of the soft function, and all logarithmic terms in the jet and soft functions up to three loops. Our result holds for C in the peak, tail, and far tail regions. Additionally, we treat hadronization effects using a field theoretic nonperturbative soft function, with moments Ω n. To eliminate an O(Λ QCD) renormalon ambiguity in themore » soft function, we switch from the MS¯ to a short distance “Rgap” scheme to define the leading power correction parameter Ω 1. We show how to simultaneously account for running effects in Ω 1 due to renormalon subtractions and hadron-mass effects, enabling power correction universality between C-parameter and thrust to be tested in our setup. We discuss in detail the impact of resummation and renormalon subtractions on the convergence. In the relevant fit region for αs(m Z) and Ω 1, the perturbative uncertainty in our cross section is ≅ 2.5% at Q=m Z.« less

Quark mass relations to four-loop order in perturbative QCD.

PubMed

Marquard, Peter; Smirnov, Alexander V; Smirnov, Vladimir A; Steinhauser, Matthias

2015-04-10

We present results for the relation between a heavy quark mass defined in the on-shell and minimal subtraction (MS[over ¯]) scheme to four-loop order. The method to compute the four-loop on-shell integral is briefly described and the new results are used to establish relations between various short-distance masses and the MS[over ¯] quark mass to next-to-next-to-next-to-leading order accuracy. These relations play an important role in the accurate determination of the MS[over ¯] heavy quark masses.

Lambda polarization feasibility study at BM@N

NASA Astrophysics Data System (ADS)

Suvarieva, Dilyna; Gudima, Konstantin; Zinchenko, Alexander

2017-03-01

Heavy strange objects (hyperons) could provide essential signatures of the excited and compressed baryonic matter. At NICA, it is planned to study hyperons both in the collider mode (MPD detector) and the fixed-target one (BM@N setup). Measurements of strange hyperons polarization could give additional information on the strong interaction mechanisms. In heavy-ion collisions, such measurements are even more valuable since the polarization is expected to be sensitive to characteristics of the QCD medium (vorticity, hydrodynamic helicity) and to QCD anomalous transport. In this analysis, the possibility to measure at BM@N the polarization of the lightest strange hyperon Λ is studied in Monte Carlo event samples produced with the DCM-QGSM generator. It is shown that the detector will allow to measure Λ polarization with a precision required to check the model predictions.

Multifunctional Dumbbell-Shaped DNA-Templated Selective Formation of Fluorescent Silver Nanoclusters or Copper Nanoparticles for Sensitive Detection of Biomolecules.

PubMed

Chen, Jinyang; Ji, Xinghu; Tinnefeld, Philip; He, Zhike

2016-01-27

In this work, a multifunctional template for selective formation of fluorescent silver nanoclusters (AgNCs) or copper nanoparticles (CuNPs) is put forward. This dumbbell-shaped (DS) DNA template is made up of two cytosine hairpin loops and an adenine-thymine-rich double-helical stem which is closed by the loops. The cytosine loops act as specific regions for the growth of AgNCs, and the double-helical stem serves as template for the CuNPs formation. By carefully investigating the sequence and length of DS DNA, we present the optimal design of the template. Benefiting from the smart design and facile synthesis, a simple, label-free, and ultrasensitive fluorescence strategy for adenosine triphosphate (ATP) detection is proposed. Through the systematic comparison, it is found that the strategy based on CuNPs formation is more sensitive for ATP assay than that based on AgNCs synthesis, and the detection limitation was found to be 81 pM. What's more, the CuNPs formation-based method is successfully applied in the detection of ATP in human serum as well as the determination of cellular ATP. In addition to small target molecule, the sensing strategy was also extended to the detection of biomacromolecule (DNA), which illustrates the generality of this biosensor.

On the Casimir scaling violation in the cusp anomalous dimension at small angle

NASA Astrophysics Data System (ADS)

Grozin, Andrey; Henn, Johannes; Stahlhofen, Maximilian

2017-10-01

We compute the four-loop n f contribution proportional to the quartic Casimir of the QCD cusp anomalous dimension as an expansion for small cusp angle ϕ. This piece is gauge invariant, violates Casimir scaling, and first appears at four loops. It requires the evaluation of genuine non-planar four-loop Feynman integrals. We present results up to O({φ}^4) . One motivation for our calculation is to probe a recent conjecture on the all-order structure of the cusp anomalous dimension. As a byproduct we obtain the four-loop HQET wave function anomalous dimension for this color structure.

NUMERICAL SIMULATIONS OF HELICITY CONDENSATION IN THE SOLAR CORONA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, L.; Zurbuchen, T. H.; DeVore, C. R.

The helicity condensation model has been proposed by Antiochos to explain the observed smoothness of coronal loops and the observed buildup of magnetic shear at filament channels. The basic hypothesis of the model is that magnetic reconnection in the corona causes the magnetic stress injected by photospheric motions to collect only at those special locations where prominences are observed to form. In this work we present the first detailed quantitative MHD simulations of the reconnection evolution proposed by the helicity condensation model. We use the well-known ansatz of modeling the closed corona as an initially uniform field between two horizontalmore » photospheric plates. The system is driven by applying photospheric rotational flows that inject magnetic helicity into the corona. The flows are confined to a finite region on the photosphere so as to mimic the finite flux system of a bipolar active region, for example. The calculations demonstrate that, contrary to common belief, opposite helicity twists do not lead to significant reconnection in such a coronal system, whereas twists with the same sense of helicity do produce substantial reconnection. Furthermore, we find that for a given amount of helicity injected into the corona, the evolution of the magnetic shear is insensitive to whether the pattern of driving photospheric motions is fixed or quasi-random. In all cases, the shear propagates via reconnection to the boundary of the flow region while the total magnetic helicity is conserved, as predicted by the model. We discuss the implications of our results for solar observations and for future, more realistic simulations of the helicity condensation process.« less

DIRECT OBSERVATIONS OF TETHER-CUTTING RECONNECTION DURING A MAJOR SOLAR EVENT FROM 2014 FEBRUARY 24 TO 25

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Huadong; Zhang, Jun; Yang, Shuhong

2014-12-20

Using multi-wavelength data from the Atmospheric Imaging Assembly on board the Solar Dynamics Observatory, we investigated two successive solar flares, a C5.1 confined flare and an X4.9 ejective flare with a halo coronal mass ejection, in NOAA active region 11990 from 2014 February 24 to 25. Before the confined flare onset, EUV brightening beneath the filament was detected. As the flare began, a twisted helical flux rope (FR) wrapping around the filament moved upward and then stopped, and in the meantime an obvious X-ray source below it was observed. Prior to the ejective X4.9 flare, some pre-existing loop structures inmore » the active region interacted with each other, which produced a brightening region beneath the filament. Meanwhile, a small flaring loop appeared below the interaction region and some new helical lines connecting the far ends of the loop structures were gradually formed and continually added into the former twisted FR. Then, due to the resulting imbalance between the magnetic pressure and tension, the new FR, together with the filament, erupted outward. Our observations coincide well with a tether-cutting model, suggesting that the two flares probably have the same triggering mechanism, i.e., tether-cutting reconnection. To our knowledge, this is the first direct observation of tether-cutting reconnection occurring between pre-existing loops in an active region. In the ejective flare case, the erupting filament exhibited an Ω-like kinked structure and underwent an exponential rise after a slow-rise phase, indicating that the kink instability might be also responsible for the eruption initiation.« less

One-loop light-cone QCD, effective action for reggeized gluons and QCD RFT calculus

NASA Astrophysics Data System (ADS)

Bondarenko, S.; Lipatov, L.; Pozdnyakov, S.; Prygarin, A.

2017-09-01

The effective action for reggeized gluons is based on the gluodynamic Yang-Mills Lagrangian with external current for longitudinal gluons added, see Lipatov (Nucl Phys B 452:369, 1995; Phys Rep 286:131, 1997; Subnucl Ser 49:131, 2013; Int J Mod Phys Conf Ser 39:1560082, 2015; Int J Mod Phys A 31(28/29):1645011, 2016; EPJ Web Conf 125:01010, 2016). On the base of classical solutions, obtained in Bondarenko et al. (Eur Phys J C 77(8):527, 2017), the one-loop corrections to this effective action in light-cone gauge are calculated. The RFT calculus for reggeized gluons similarly to the RFT introduced in Gribov (Sov Phys JETP 26:414, 1968) is proposed and discussed. The correctness of the results is verified by calculation of the propagators of A+ and A- reggeized gluons fields and application of the obtained results is discussed as well.

Probing the Self-Assembly and the Accompanying Structural Changes of Hydrophobin SC3 on a Hydrophobic Surface by Mass Spectrometry

PubMed Central

Wang, X.; Permentier, H. P.; Rink, R.; Kruijtzer, J. A. W.; Liskamp, R. M. J.; Wösten, H. A. B.; Poolman, B.; Robillard, G. T.

2004-01-01

The fungal class I hydrophobin SC3 self-assembles into an amphipathic membrane at hydrophilic-hydrophobic interfaces such as the water-air and water-Teflon interface. During self-assembly, the water-soluble state of SC3 proceeds via the intermediate α-helical state to the stable end form called the β-sheet state. Self-assembly of the hydrophobin at the Teflon surface is arrested in the α-helical state. The β-sheet state can be induced at elevated temperature in the presence of detergent. The structural changes of SC3 were monitored by various mass spectrometry techniques. We show that the so-called second loop of SC3 (C39–S72) has a high affinity for Teflon. Binding of this part of SC3 to Teflon was accompanied by the formation of α-helical structure and resulted in low solvent accessibility. The solvent-protected region of the second loop extended upon conversion to the β-sheet state. In contrast, the C-terminal part of SC3 became more exposed to the solvent. The results indicate that the second loop of class I hydrophobins plays a pivotal role in self-assembly at the hydrophilic-hydrophobic interface. Of interest, this loop is much smaller in case of class II hydrophobins, which may explain the differences in their assembly. PMID:15345568

Running of the charm-quark mass from HERA deep-inelastic scattering data

DOE PAGES

Gizhko, A.; Geiser, A.; Moch, S.; ...

2017-11-07

Combined HERA data on charm production in deep-inelastic scattering have previously been used to determine the charm-quark running mass m c(m c) in the MS¯ renormalisation scheme. Here, the same data are used as a function of the photon virtuality Q 2 to evaluate the charm-quark running mass at different scales to one-loop order, in the context of a next-to-leading order QCD analysis. Lastly, the scale dependence of the mass is found to be consistent with QCD expectations.

Running of the charm-quark mass from HERA deep-inelastic scattering data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gizhko, A.; Geiser, A.; Moch, S.

Combined HERA data on charm production in deep-inelastic scattering have previously been used to determine the charm-quark running mass m c(m c) in the MS¯ renormalisation scheme. Here, the same data are used as a function of the photon virtuality Q 2 to evaluate the charm-quark running mass at different scales to one-loop order, in the context of a next-to-leading order QCD analysis. Lastly, the scale dependence of the mass is found to be consistent with QCD expectations.

Complex heavy-quark potential at finite temperature from lattice QCD.

PubMed

Rothkopf, Alexander; Hatsuda, Tetsuo; Sasaki, Shoichi

2012-04-20

We calculate for the first time the complex potential between a heavy quark and antiquark at finite temperature across the deconfinement transition in lattice QCD. The real and imaginary part of the potential at each separation distance r is obtained from the spectral function of the thermal Wilson loop. We confirm the existence of an imaginary part above the critical temperature T(C), which grows as a function of r and underscores the importance of collisions with the gluonic environment for the melting of heavy quarkonia in the quark-gluon plasma.

Hadronic light-by-light scattering contribution to the muon anomalous magnetic moment from lattice QCD

DOE PAGES

Blum, Thomas; Chowdhury, Saumitra; Hayakawa, Masashi; ...

2015-01-07

The form factor that yields the light-by-light scattering contribution to the muon anomalous magnetic moment is computed in lattice QCD+QED and QED. A non-perturbative treatment of QED is used and is checked against perturbation theory. The hadronic contribution is calculated for unphysical quark and muon masses, and only the diagram with a single quark loop is computed. Statistically significant signals are obtained. Initial results appear promising, and the prospect for a complete calculation with physical masses and controlled errors is discussed.

Comparative NMR Analysis of an 80-Residue G Protein-Coupled Receptor Fragment in Two Membrane Mimetic Environments

PubMed Central

LS, Cohen; B, Arshava; A, Neumoin; JM, Becker; P, Güntert; O, Zerbe; Naider, F

2011-01-01

Fragments of integral membrane proteins have been used to study the physical chemical properties of regions of transporters and receptors. Ste2p(G31-T110) is an 80-residue polypeptide which contains a portion of the N-terminal domain, transmembrane domain 1 (TM1), intracellular loop 1, TM2 and part of extracellular loop 2 of the α-factor receptor (Ste2p) from Saccharomyces cerevisiae. The structure of this peptide was previously determined to form a helical hairpin in lyso-palmitoylphosphatidyl-glycerol micelles (LPPG)[1]. Herein, we perform a systematic comparison of the structure of this protein fragment in micelles and trifluoroethanol(TFE):water in order to understand whether spectra recorded in organic:aqueous medium can facilitate the structure determination in a micellar environment. Using uniformly labeled peptide and peptide selectively protonated on Ile, Val and Leu methyl groups in a perdeuterated background and a broad set of 3D NMR experiments we assigned 89% of the observable atoms. NOEs and chemical shift analysis were used to define the helical regions of the fragment. Together with constraints from paramagnetic spin labeling, NOEs were used to calculate a transiently folded helical hairpin structure for this peptide in TFE:water. Correlation of chemical shifts was insufficient to transfer assignments from TFE:water to LPPG spectra in the absence of further information. PMID:21791199

Insights into the Photoprotective Switch of the Major Light-harvesting Complex II (LHCII)

PubMed Central

Sunku, Kiran; de Groot, Huub. J. M.; Pandit, Anjali

2013-01-01

Light-harvesting antennae of the LHC family form transmembrane three-helix bundles of which two helices are interlocked by conserved arginine-glutamate (Arg-Glu) ion pairs that form ligation sites for chlorophylls. The antenna proteins of photosystem II have an intriguing dual function. In excess light, they can switch their conformation from a light-harvesting into a photoprotective state, in which the excess and harmful excitation energies are safely dissipated as heat. Here we applied magic angle spinning NMR and selective Arg isotope enrichment as a noninvasive method to analyze the Arg structures of the major light-harvesting complex II (LHCII). The conformations of the Arg residues that interlock helix A and B appear to be preserved in the light-harvesting and photoprotective state. Several Arg residues have very downfield-shifted proton NMR responses, indicating that they stabilize the complex by strong hydrogen bonds. For the Arg Cα chemical shifts, differences are observed between LHCII in the active, light-harvesting and in the photoprotective, quenched state. These differences are attributed to a conformational change of the Arg residue in the stromal loop region. We conclude that the interlocked helices of LHCII form a rigid core. Consequently, the LHCII conformational switch does not involve changes in A/B helix tilting but likely involves rearrangements of the loops and helical segments close to the stromal and lumenal ends. PMID:23629658

Higgs boson gluon-fusion production in QCD at three loops.

PubMed

Anastasiou, Charalampos; Duhr, Claude; Dulat, Falko; Herzog, Franz; Mistlberger, Bernhard

2015-05-29

We present the cross section for the production of a Higgs boson at hadron colliders at next-to-next-to-next-to-leading order (N^{3}LO) in perturbative QCD. The calculation is based on a method to perform a series expansion of the partonic cross section around the threshold limit to an arbitrary order. We perform this expansion to sufficiently high order to obtain the value of the hadronic cross at N^{3}LO in the large top-mass limit. For renormalization and factorization scales equal to half the Higgs boson mass, the N^{3}LO corrections are of the order of +2.2%. The total scale variation at N^{3}LO is 3%, reducing the uncertainty due to missing higher order QCD corrections by a factor of 3.

The structural coupling between ATPase activation and recovery stroke in the myosin II motor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koppole, Sampath; Smith, Jeremy C; Fischer, S.

2007-07-01

Before the myosin motor head can perform the next power stroke, it undergoes a large conformational transition in which the converter domain, bearing the lever arm, rotates {approx} 65{sup o}. Simultaneous with this 'recovery stroke', myosin activates its ATPase function by closing the Switch-2 loop over the bound ATP. This coupling between the motions of the converter domain and of the 40 {angstrom}-distant Switch-2 loop is essential to avoid unproductive ATP hydrolysis. The coupling mechanism is determined here by finding a series of optimized intermediates between crystallographic end structures of the recovery stroke (Dictyostelium discoideum), yielding movies of the transitionmore » at atomic detail. The successive formation of two hydrogen bonds by the Switch-2 loop is correlated with the successive see-saw motions of the relay and SH1 helices that hold the converter domain. SH1 helix and Switch-2 loop communicate via a highly conserved loop that wedges against the SH1-helix upon Switch-2 closing.« less

The structural coupling between ATPase activation and recovery stroke in the myosin II motor.

PubMed

Koppole, Sampath; Smith, Jeremy C; Fischer, Stefan

2007-07-01

Before the myosin motor head can perform the next power stroke, it undergoes a large conformational transition in which the converter domain, bearing the lever arm, rotates approximately 65 degrees . Simultaneous with this "recovery stroke," myosin activates its ATPase function by closing the Switch-2 loop over the bound ATP. This coupling between the motions of the converter domain and of the 40 A-distant Switch-2 loop is essential to avoid unproductive ATP hydrolysis. The coupling mechanism is determined here by finding a series of optimized intermediates between crystallographic end structures of the recovery stroke (Dictyostelium discoideum), yielding movies of the transition at atomic detail. The successive formation of two hydrogen bonds by the Switch-2 loop is correlated with the successive see-saw motions of the relay and SH1 helices that hold the converter domain. SH1 helix and Switch-2 loop communicate via a highly conserved loop that wedges against the SH1-helix upon Switch-2 closing.

Spin, twist and hadron structure in deep inelastic processes

NASA Astrophysics Data System (ADS)

Jaffe, R. L.; Meyer, H.; Piller, G.

These notes provide an introduction to polarization effects in deep inelastic processes in QCD. We emphasize recent work on transverse asymmetries, subdominant effects, and the role of polarization in fragmentation and in purely hadronic processes. After a review of kinematics and some basic tools of short distance analysis, we study the twist, helicity, chirality and transversity dependence of a variety of high energy processes sensitive to the quark and gluon substructure of hadrons.

Regge spectra of excited mesons, harmonic confinement, and QCD vacuum structure

NASA Astrophysics Data System (ADS)

Nedelko, Sergei N.; Voronin, Vladimir E.

2016-05-01

An approach to QCD vacuum as a medium describable in terms of a statistical ensemble of almost everywhere homogeneous Abelian (anti-)self-dual gluon fields is briefly reviewed. These fields play the role of the confining medium for color charged fields as well as underline the mechanism of realization of chiral S UL(Nf)×S UR(Nf) and UA(1 ) symmetries. Hadronization formalism based on this ensemble leads to manifestly defined quantum effective meson action. Strong, electromagnetic, and weak interactions of mesons are represented in the action in terms of nonlocal n -point interaction vertices given by the quark-gluon loops averaged over the background ensemble. New systematic results for the mass spectrum and decay constants of radially excited light, heavy-light mesons, and heavy quarkonia are presented. The interrelation between the present approach, models based on ideas of soft-wall anti-de Sitter/QCD, light-front holographic QCD, and the picture of harmonic confinement is outlined.

Two-body decays of gluino at full one-loop level in the quark-flavour violating MSSM.

PubMed

Eberl, Helmut; Ginina, Elena; Hidaka, Keisho

2017-01-01

We study the two-body decays of the gluino at full one-loop level in the Minimal Supersymmetric Standard Model with quark-flavour violation (QFV) in the squark sector. The renormalisation is done in the [Formula: see text] scheme. The gluon and photon radiations are included by adding the corresponding three-body decay widths. We discuss the dependence of the gluino decay widths on the QFV parameters. The main dependence stems from the [Formula: see text]-[Formula: see text] mixing in the decays to up-type squarks, and from the [Formula: see text]-[Formula: see text] mixing in the decays to down-type squarks due to the strong constraints from B-physics on the other quark-flavour-mixing parameters. The full one-loop corrections to the gluino decay widths are mostly negative and of the order of about -10%. The QFV part stays small in the total width but can vary up to -8% for the decay width into the lightest [Formula: see text] squark. For the corresponding branching ratio the effect is somehow washed out by at least a factor of two. The electroweak corrections can be as large as 35% of the SUSY QCD corrections.

Generation of helical magnetic field in a viable scenario of inflationary magnetogenesis

NASA Astrophysics Data System (ADS)

Sharma, Ramkishor; Subramanian, Kandaswamy; Seshadri, T. R.

2018-04-01

We study the generation of helical magnetic fields in a model of inflationary magnetogenesis which is free from the strong coupling and backreaction problems. To generate helical magnetic fields, we add an f2F˜μ νFμ ν term to the Lagrangian of the Ratra model. The strong coupling and backreaction problems are avoided if we take a particular behavior of coupling function f , in which f increases during inflation and decreases postinflation to reheating. The generated magnetic field is fully helical and has a blue spectrum, d ρB/d ln k ∝k4. This spectrum is obtained when coupling function f ∝a2 during inflation. The scale of reheating in our model has to be lower than 4000 GeV to avoid backreaction postinflation. The generated magnetic field spectrum satisfies the γ -ray bound for all the possible scales of reheating. The comoving magnetic field strength and its correlation length are ˜4 ×10-11 G and 70 kpc respectively, if reheating takes place at 100 GeV. For reheating at the QCD scales of 150 MeV, the field strength increases to ˜ nano gauss, with coherence scale of 0.6 Mpc.

On-the-fly reduction of open loops

NASA Astrophysics Data System (ADS)

Buccioni, Federico; Pozzorini, Stefano; Zoller, Max

2018-01-01

Building on the open-loop algorithm we introduce a new method for the automated construction of one-loop amplitudes and their reduction to scalar integrals. The key idea is that the factorisation of one-loop integrands in a product of loop segments makes it possible to perform various operations on-the-fly while constructing the integrand. Reducing the integrand on-the-fly, after each segment multiplication, the construction of loop diagrams and their reduction are unified in a single numerical recursion. In this way we entirely avoid objects with high tensor rank, thereby reducing the complexity of the calculations in a drastic way. Thanks to the on-the-fly approach, which is applied also to helicity summation and for the merging of different diagrams, the speed of the original open-loop algorithm can be further augmented in a very significant way. Moreover, addressing spurious singularities of the employed reduction identities by means of simple expansions in rank-two Gram determinants, we achieve a remarkably high level of numerical stability. These features of the new algorithm, which will be made publicly available in a forthcoming release of the OpenLoops program, are particularly attractive for NLO multi-leg and NNLO real-virtual calculations.

Local Helicity Injection Systems for Non-solenoidal Startup in the PEGASUS Toroidal Experiment

NASA Astrophysics Data System (ADS)

Perry, J. M.; Barr, J. L.; Bongard, M. W.; Fonck, R. J.; Hinson, E. T.; Lewicki, B. T.; Redd, A. J.

2013-10-01

Local helicity injection is being developed in the PEGASUS Toroidal Experiment for non-solenoidal startup in spherical tokamaks. The effective loop voltage due to helicity injection scales with the area of the injectors, requiring the development of electron current injectors with areas much larger than the 2 cm2 plasma arc injectors used to date. Solid and gas-effused metallic electrodes were found to be unusable due to reduced injector area utilization from localized cathode spots and narrow operational regimes. An integrated array of 8 compact plasma arc sources is thus being developed for high current startup. It employs two monolithic power systems, for the plasma arc sources and the bias current extraction system. The array effectively eliminates impurity fueling from plasma-material interaction by incorporating a local scraper-limiter and conical-frustum bias electrodes to mitigate the effects of cathode spots. An energy balance model of helicity injection indicates that the resulting 20 cm2 of total injection area should provide sufficient current drive to reach 0.3 MA. At that level, helicity injection drive exceeds that from poloidal induction, which is the relevant operational regime for large-scale spherical tokamaks. Future placement of the injector array near an expanded boundary divertor region will test simultaneous optimization of helicity drive and the Taylor relaxation current limit. Work supported by US DOE Grant DE-FG02-96ER54375.

Polyakov loop fluctuations in the presence of external fields

NASA Astrophysics Data System (ADS)

Lo, Pok Man; Szymański, Michał; Redlich, Krzysztof; Sasaki, Chihiro

2018-06-01

We study the implications of the spontaneous and explicit Z(3) center symmetry breaking for the Polyakov loop susceptibilities. To this end, ratios of the susceptibilities of the real and imaginary parts, as well as of the modulus of the Polyakov loop are computed within an effective model using a color group integration scheme. We show that the essential features of the lattice QCD results of these ratios can be successfully captured by the effective approach. Furthermore we discuss a novel scaling relation in one of these ratios involving the explicit breaking field, volume, and temperature.

The principle of maximal transcendentality and the four-loop collinear anomalous dimension

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dixon, Lance J.

Here, we use the principle of maximal transcendentality and the universal nature of subleading infrared poles to extract the analytic value of the four-loop collinear anomalous dimension in planar N = 4 super-Yang-Mills theory from recent QCD results, obtainingmore » $$\\hat{g}$$$(4)\\atop{0}$$ =$-$300ζ 7$-$256ζ 2ζ 5$-$384ζ 3ζ 4. This value agrees with a previous numerical result to within 0.2%. It also provides the Regge trajectory, threshold soft anomalous dimension and rapidity anomalous dimension through four loops.« less

The principle of maximal transcendentality and the four-loop collinear anomalous dimension

DOE PAGES

Dixon, Lance J.

2018-01-16

Here, we use the principle of maximal transcendentality and the universal nature of subleading infrared poles to extract the analytic value of the four-loop collinear anomalous dimension in planar N = 4 super-Yang-Mills theory from recent QCD results, obtainingmore » $$\\hat{g}$$$(4)\\atop{0}$$ =$-$300ζ 7$-$256ζ 2ζ 5$-$384ζ 3ζ 4. This value agrees with a previous numerical result to within 0.2%. It also provides the Regge trajectory, threshold soft anomalous dimension and rapidity anomalous dimension through four loops.« less

A Monte Carlo Study of Lambda Hyperon Polarization at BM@N

NASA Astrophysics Data System (ADS)

Suvarieva, D.; Gudima, K.; Zinchenko, A.

2018-03-01

Heavy strange objects (hyperons) can provide essential signatures of the excited and compressed baryonic matter. At NICA, it is planned to study hyperons both in the collider mode (MPD detector) and the fixed-target one (BM@N setup). Measurements of strange hyperon polarization can give additional information on the strong interaction mechanisms. In heavy-ion collisions, such measurements are even more valuable since the polarization is expected to be sensitive to characteristics of the QCD medium (vorticity, hydrodynamic helicity) and to QCD anomalous transport. In this analysis, the possibility to measure at BM@N the polarization of the lightest strange hyperon Λ is studied in Monte Carlo event samples of Au + Au collisions produced with the DCM-QGSM generator. It is shown that the detector will allow to measure polarization with a precision required to check the model predictions.

Structural characterization of the H-NS protein from Xylella fastidiosa and its interaction with DNA.

PubMed

Rosselli-Murai, Luciana K; Sforça, Maurício L; Sassonia, Rogério C; Azzoni, Adriano R; Murai, Marcelo J; de Souza, Anete P; Zeri, Ana C

2012-10-01

The nucleoid-associated protein H-NS is a major component of the bacterial nucleoid involved in DNA compaction and transcription regulation. The NMR solution structure of the Xylella fastidiosa H-NS C-terminal domain (residues 56-134) is presented here and consists of two beta-strands and two alpha helices, with one loop connecting the two beta-strands and a second loop connecting the second beta strand and the first helix. The amide (1)H and (15)N chemical shift signals for a sample of XfH-NS(56-134) were monitored in the course of a titration series with a 14-bp DNA duplex. Most of the residues involved in contacts to DNA are located around the first and second loops and in the first helix at a positively charged side of the protein surface. The overall structure of the Xylella H-NS C-terminal domain differ significantly from Escherichia coli and Salmonella enterica H-NS proteins, even though the DNA binding motif in loop 2 adopt similar conformation, as well as β-strand 2 and loop 1. Interestingly, we have also found that the DNA binding site is expanded to include helix 1, which is not seen in the other structures. Copyright © 2012 Elsevier Inc. All rights reserved.

Simultaneous Determination of Two Subdomain Folding Rates Using the "Transfer-Quench" Method.

PubMed

Rahamim, Gil; Amir, Dan; Haas, Elisha

2017-05-09

The investigation of the mechanism of protein folding is complicated by the context dependence of the rates of intramolecular contact formation. Methods based on site-specific labeling and ultrafast spectroscopic detection of fluorescence signals were developed for monitoring the rates of individual subdomain folding transitions in situ, in the context of the whole molecule. However, each site-specific labeling modification might affect rates of folding of near-neighbor structural elements, and thus limit the ability to resolve fine differences in rates of folding of these elements. Therefore, it is highly desirable to be able to study the rates of folding of two or more neighboring subdomain structures using a single mutant to facilitate resolution of the order and interdependence of such steps. Here, we report the development of the "Transfer-Quench" method for measuring the rate of formation of two structural elements using a single triple-labeled mutant. This method is based on Förster resonance energy transfer combined with fluorescence quenching. We placed the donor and acceptor at the loop ends, and a quencher at an α-helical element involved in the node forming the loop. The folding of the triple-labeled mutant is monitored by the acceptor emission. The formation of nonlocal contact (loop closure) increases the time-dependent acceptor emission, while the closure of the labeled helix turn reduces this emission. The method was applied in a study of the folding mechanism of the common model protein, the B domain of staphylococcal protein A. Only natural amino acids were used as probes, and thus possible structural perturbations were minimized. Tyr and Trp residues served as donor and acceptor at the ends of a long loop between helices I and II, and a Cys residue as a quencher for the acceptor. We found that the closure of the loop (segment 14-33) occurs with the same rate constant as the nucleation of helix HII (segment 33-29), in line with the nucleation-condensation model. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Efficient numerical evaluation of Feynman integrals

NASA Astrophysics Data System (ADS)

Li, Zhao; Wang, Jian; Yan, Qi-Shu; Zhao, Xiaoran

2016-03-01

Feynman loop integrals are a key ingredient for the calculation of higher order radiation effects, and are responsible for reliable and accurate theoretical prediction. We improve the efficiency of numerical integration in sector decomposition by implementing a quasi-Monte Carlo method associated with the CUDA/GPU technique. For demonstration we present the results of several Feynman integrals up to two loops in both Euclidean and physical kinematic regions in comparison with those obtained from FIESTA3. It is shown that both planar and non-planar two-loop master integrals in the physical kinematic region can be evaluated in less than half a minute with accuracy, which makes the direct numerical approach viable for precise investigation of higher order effects in multi-loop processes, e.g. the next-to-leading order QCD effect in Higgs pair production via gluon fusion with a finite top quark mass. Supported by the Natural Science Foundation of China (11305179 11475180), Youth Innovation Promotion Association, CAS, IHEP Innovation (Y4545170Y2), State Key Lab for Electronics and Particle Detectors, Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China (Y4KF061CJ1), Cluster of Excellence Precision Physics, Fundamental Interactions and Structure of Matter (PRISMA-EXC 1098)

Analysis of inter-residue contacts reveals folding stabilizers in P-loops of potassium, sodium, and TRPV channels.

PubMed

Korkosh, V S; Zhorov, B S; Tikhonov, D B

2016-05-01

The family of P-loop channels includes potassium, sodium, calcium, cyclic nucleotide-gated and TRPV channels, as well as ionotropic glutamate receptors. Despite vastly different physiological and pharmacological properties, the channels have structurally conserved folding of the pore domain. Furthermore, crystallographic data demonstrate surprisingly similar mutual disposition of transmembrane and membrane-diving helices. To understand determinants of this conservation, here we have compared available high-resolution structures of sodium, potassium, and TRPV1 channels. We found that some residues, which are in matching positions of the sequence alignment, occur in different positions in the 3D alignment. Surprisingly, we found 3D mismatches in well-packed P-helices. Analysis of energetics of individual residues in Monte Carlo minimized structures revealed cyclic patterns of energetically favorable inter- and intra-subunit contacts of P-helices with S6 helices. The inter-subunit contacts are rather conserved in all the channels, whereas the intra-subunit contacts are specific for particular types of the channels. Our results suggest that these residue-residue contacts contribute to the folding stabilization. Analysis of such contacts is important for structural and phylogenetic studies of homologous proteins.

CD and NMR conformational studies of a peptide encompassing the Mid Loop interface of Ship2-Sam.

PubMed

Mercurio, Flavia A; Scognamiglio, Pasqualina L; Di Natale, Concetta; Marasco, Daniela; Pellecchia, Maurizio; Leone, Marilisa

2014-11-01

The lipid phosphatase Ship2 is a protein that intervenes in several diseases such as diabetes, cancer, neurodegeneration, and atherosclerosis. It is made up of a catalytic domain and several protein docking modules such as a C-terminal Sam (Sterile alpha motif) domain. The Sam domain of Ship2 (Ship2-Sam) binds to the Sam domains of the EphA2 receptor (EphA2-Sam) and the PI3K effector protein Arap3 (Arap3-Sam). These heterotypic Sam-Sam interactions occur through formation of dimers presenting the canonical "Mid Loop/End Helix" binding mode. The central region of Ship2-Sam, spanning the C-terminal end of α2, the α3 and α4 helices together with the α2α3 and α3α4 interhelical loops, forms the Mid Loop surface that is needed to bind partners Sam domains. A peptide encompassing most of the Ship2-Sam Mid Loop interface (Shiptide) capable of binding to both EphA2-Sam and Arap3-Sam, was previously identified. Here we investigated the conformational features of this peptide, through solution CD and NMR studies in different conditions. These studies reveal that the peptide is highly flexible in aqueous buffer, while it adopts a helical conformation in presence of 2,2,2-trifluoroethanol. The discovered structural insights and in particular the identification of a helical motif, may lead to the design of more constrained and possibly cell permeable Shiptide analogs that could work as efficient antagonists of Ship2-Sam heterotypic interactions and embrace therapeutic applications. © 2014 Wiley Periodicals, Inc.

Hard Break-Up of Two-Nucleons and QCD Dynamics of NN Interaction

NASA Astrophysics Data System (ADS)

Sargsian, Misak

2008-10-01

We discus recent developments in theory of high energy two-body break-up of few-nucleon systems. The characteristics of these reactions are such that the hard two-body quasielastic subprocess can be clearly separated from the accompanying soft subprocesses. We discuss in details the hard rescattering model (HRM) in which hard photodisintegration develops in two stages. At first, photon knocks-out an energetic quark which rescatters subsequently with a quark of the other nucleon. The latter provides a mechanism of sharing the initial high momentum of the photon between two outgoing nucleons. This final state hard rescattering can be expressed through the hard NN scattering amplitude. Within HRM we discuss hard break-up reactions involving D and 3He targets and demonstrate how these reactions are sensitive to the dynamics of hard pn and pp interaction. Another development of HRM is the prediction of new helicity selection mechanism for hard two-body reactions, which was apparently confirmed in the recent JLab experiment.

The singular behavior of massive QCD amplitudes

NASA Astrophysics Data System (ADS)

Mitov, Alexander; Moch, Sven-Olaf

2007-05-01

We discuss the structure of infrared singularities in on-shell QCD amplitudes with massive partons and present a general factorization formula in the limit of small parton masses. The factorization formula gives rise to an all-order exponentiation of both, the soft poles in dimensional regularization and the large collinear logarithms of the parton masses. Moreover, it provides a universal relation between any on-shell amplitude with massive external partons and its corresponding massless amplitude. For the form factor of a heavy quark we present explicit results including the fixed-order expansion up to three loops in the small mass limit. For general scattering processes we show how our constructive method applies to the computation of all singularities as well as the constant (mass-independent) terms of a generic massive n-parton QCD amplitude up to the next-to-next-to-leading order corrections.

The interaction between the yeast telomerase RNA and the Est1 protein requires three structural elements.

PubMed

Lubin, Johnathan W; Tucey, Timothy M; Lundblad, Victoria

2012-09-01

In the budding yeast Saccharomyces cerevisiae, the telomerase enzyme is composed of a 1.3-kb TLC1 RNA that forms a complex with Est2 (the catalytic subunit) and two regulatory proteins, Est1 and Est3. Previous work has identified a conserved 5-nt bulge, present in a long helical arm of TLC1, which mediates binding of Est1 to TLC1. However, increased expression of Est1 can bypass the consequences of removal of this RNA bulge, indicating that there are additional binding site(s) for Est1 on TLC1. We report here that a conserved single-stranded internal loop immediately adjacent to the bulge is also required for the Est1-RNA interaction; furthermore, a TLC1 variant that lacks this internal loop but retains the bulge cannot be suppressed by Est1 overexpression, arguing that the internal loop may be a more critical element for Est1 binding. An additional structural feature consisting of a single-stranded region at the base of the helix containing the bulge and internal loop also contributes to recognition of TLC1 by Est1, potentially by providing flexibility to this helical arm. Association of Est1 with each of these TLC1 motifs was assessed using a highly sensitive biochemical assay that simultaneously monitors the relative levels of the Est1 and Est2 proteins in the telomerase complex. The identification of three elements of TLC1 that are required for Est1 association provides a detailed view of this particular protein-RNA interaction.

A SOLAR TORNADO OBSERVED BY AIA/SDO: ROTATIONAL FLOW AND EVOLUTION OF MAGNETIC HELICITY IN A PROMINENCE AND CAVITY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Xing; Morgan, Huw; Leonard, Drew

During 2011 September 24, as observed by the Atmospheric Imaging Assembly instrument of the Solar Dynamic Observatory and ground-based H{alpha} telescopes, a prominence and associated cavity appeared above the southwest limb. On 2011 September 25 8:00 UT, material flows upward from the prominence core along a narrow loop-like structure, accompanied by a rise ({>=}50,000 km) of the prominence core and the loop. As the loop fades by 10:00, small blobs and streaks of varying brightness rotate around the top part of the prominence and cavity, mimicking a cyclone. The most intense and coherent rotation lasts for over three hours, withmore » emission in both hot ({approx}1 MK) and cold (hydrogen and helium) lines. We suggest that the cyclonic appearance and overall evolution of the structure can be interpreted in terms of the expansion of helical structures into the cavity, and the movement of plasma along helical structures which appears as a rotation when viewed along the helix axis. The coordinated movement of material between prominence and cavity suggests that they are structurally linked. Complexity is great due to the combined effect of these actions and the line-of-sight integration through the structure which contains tangled fields.« less

Structural plasticity of 4-α-helical bundles exemplified by the puzzle-like molecular assembly of the Rop protein

PubMed Central

Amprazi, Maria; Kotsifaki, Dina; Providaki, Mary; Kapetaniou, Evangelia G.; Fellas, Georgios; Kyriazidis, Ioannis; Pérez, Javier; Kokkinidis, Michael

2014-01-01

The dimeric Repressor of Primer (Rop) protein, a widely used model system for the study of coiled-coil 4-α-helical bundles, is characterized by a remarkable structural plasticity. Loop region mutations lead to a wide range of topologies, folding states, and altered physicochemical properties. A protein-folding study of Rop and several loop variants has identified specific residues and sequences that are linked to the observed structural plasticity. Apart from the native state, native-like and molten-globule states have been identified; these states are sensitive to reducing agents due to the formation of nonnative disulfide bridges. Pro residues in the loop are critical for the establishment of new topologies and molten globule states; their effects, however, can be in part compensated by Gly residues. The extreme plasticity in the assembly of 4-α-helical bundles reflects the capacity of the Rop sequence to combine a specific set of hydrophobic residues into strikingly different hydrophobic cores. These cores include highly hydrated ones that are consistent with the formation of interchain, nonnative disulfide bridges and the establishment of molten globules. Potential applications of this structural plasticity are among others in the engineering of bio-inspired materials. PMID:25024213

Molecular dynamics simulations of electrostatics and hydration distributions around RNA and DNA motifs

NASA Astrophysics Data System (ADS)

Marlowe, Ashley E.; Singh, Abhishek; Semichaevsky, Andrey V.; Yingling, Yaroslava G.

2009-03-01

Nucleic acid nanoparticles can self-assembly through the formation of complementary loop-loop interactions or stem-stem interactions. Presence and concentration of ions can significantly affect the self-assembly process and the stability of the nanostructure. In this presentation we use explicit molecular dynamics simulations to examine the variations in cationic distributions and hydration environment around DNA and RNA helices and loop-loop interactions. Our simulations show that the potassium and sodium ionic distributions are different around RNA and DNA motifs which could be indicative of ion mediated relative stability of loop-loop complexes. Moreover in RNA loop-loop motifs ions are consistently present and exchanged through a distinct electronegative channel. We will also show how we used the specific RNA loop-loop motif to design a RNA hexagonal nanoparticle.

HIGH TEMPERATURE REACTOR

DOEpatents

Kulsrud, R.M.; Spitzer, L. Jr.

1961-12-12

An apparatus of the stellarator type for heating a plasma to high temperatures is designed. Circularizers at the end of then helical windings produce a circular magnetic surface and provide improved confining and heating of the plasma. Reverse curvature sections formed in the end loops of the reaction tube provide increased plasma pressure for a given magnetic field pressure and thereby minimize the current flow in the helical windings. (AEC)

NLO QCD predictions for Z+γ + jets production with Sherpa

NASA Astrophysics Data System (ADS)

Krause, Johannes; Siegert, Frank

2018-02-01

We present precise predictions for prompt photon production in association with a Z boson and jets. They are obtained within the Sherpa framework as a consistently merged inclusive sample. Leptonic decays of the Z boson are fully included in the calculation with all off-shell effects. Virtual matrix elements are provided by OpenLoops and parton-shower effects are simulated with a dipole parton shower. Thanks to the NLO QCD corrections included not only for inclusive Zγ production but also for the Zγ + 1-jet process we find significantly reduced systematic uncertainties and very good agreement with experimental measurements at √{s}=8 TeV. Predictions at √{s}=13 TeV are displayed including a study of theoretical uncertainties. In view of an application of these simulations within LHC experiments, we discuss in detail the necessary combination with a simulation of the Z + jets final state. In addition to a corresponding prescription we introduce recommended cross checks to avoid common pitfalls during the overlap removal between the two samples.

Soft thermal contributions to 3-loop gauge coupling

NASA Astrophysics Data System (ADS)

Laine, M.; Schicho, P.; Schröder, Y.

2018-05-01

We analyze 3-loop contributions to the gauge coupling felt by ultrasoft ("magnetostatic") modes in hot Yang-Mills theory. So-called soft/hard terms, originating from dimension-six operators within the soft effective theory, are shown to cancel 1097/1098 of the IR divergence found in a recent determination of the hard 3-loop contribution to the soft gauge coupling. The remaining 1/1098 originates from ultrasoft/hard contributions, induced by dimension-six operators in the ultrasoft effective theory. Soft 3-loop contributions are likewise computed, and are found to be IR divergent, rendering the ultrasoft gauge coupling non-perturbative at relative order O({α}s^{3/2}) . We elaborate on the implications of these findings for effective theory studies of physical observables in thermal QCD.

Top-quark loop corrections in Z+jet and Z + 2 jet production

DOE Office of Scientific and Technical Information (OSTI.GOV)

Campbell, John M.; Keith Ellis, R.

2017-01-01

The sophistication of current predictions formore » $Z+$jet production at hadron colliders necessitates a re-evaluation of any approximations inherent in the theoretical calculations. In this paper we address one such issue, the inclusion of mass effects in top-quark loops. We ameliorate an existing calculation of $Z+1$~jet and $Z+2$~jet production by presenting exact analytic formulae for amplitudes containing top-quark loops that enter at next-to-leading order in QCD. Although approximations based on an expansion in powers of $$1/m_t^2$$ can lead to poor high-energy behavior, an exact treatment of top-quark loops demonstrates that their effect is small and has limited phenomenological interest.« less

NLO cross sections in 4 dimensions without DREG

NASA Astrophysics Data System (ADS)

Hernández-Pinto, R. J.; Driencourt-Mangin, F.; Rodrigo, G.; Sborlini, G. F. R.

2016-10-01

In this review, we present a new method for computing physical cross sections at NLO accuracy in QCD without using the standard Dimensional Regularisation. The algorithm is based on the Loop-Tree Duality theorem, which allow us to obtain loop integrals as a sum of phase-space integrals; in this way, transforming loop integrals into phase-space integrals, we propose a method to merge virtual and real contributions in order to find observables at NLO in d = 4 space-time dimensions. In addition, the strategy described is used for computing the γ* → qq̅(g) process. A more detailed discussion related on this topic can be found in Ref [1].

The helical MreB cytoskeleton in Escherichia coli MC1000/pLE7 is an artifact of the N-Terminal yellow fluorescent protein tag.

PubMed

Swulius, Matthew T; Jensen, Grant J

2012-12-01

Based on fluorescence microscopy, the actin homolog MreB has been thought to form extended helices surrounding the cytoplasm of rod-shaped bacterial cells. The presence of these and other putative helices has come to dominate models of bacterial cell shape regulation, chromosome segregation, polarity, and motility. Here we use electron cryotomography to show that MreB does in fact form extended helices and filaments in Escherichia coli when yellow fluorescent protein (YFP) is fused to its N terminus but native (untagged) MreB expressed to the same levels does not. In contrast, mCherry fused to an internal loop (MreB-RFP(SW)) does not induce helices. The helices are therefore an artifact of the placement of the fluorescent protein tag. YFP-MreB helices were also clearly distinguishable from the punctate, "patchy" localization patterns of MreB-RFP(SW), even by standard light microscopy. The many interpretations in the literature of such punctate patterns as helices should therefore be reconsidered.

A novel representation of the conformational structure of transfer RNAs. Correlation of the folding patterns of the polynucleotide chain with the base sequence and the nucleotide backbone torsions.

PubMed Central

Srinivasan, A R; Yathindra, N

1977-01-01

A novel description of the conformational characteristics of all the individual nucleotides and the phosphodiesters in tRNAs is presented in the form of a circular plot. This representation furnishes information of the base sequence with the folding patterns of the polynucleotide chain as one traverses along the circumference and with the individual nucleotide and phosphodiester linkage torsions along the radii. The circular plot obtained for yeast tRNAPhe strikingly distinguishes the helical and the loop regions. The variation of the different nucleotide torsions along the entire chain length and their effect on the secondary helical and tertiary loop regions become readily apparent. PMID:339206

Study of ordered hadron chains with the ATLAS detector

NASA Astrophysics Data System (ADS)

Aaboud, M.; Aad, G.; Abbott, B.; Abdinov, O.; Abeloos, B.; Abidi, S. H.; Abouzeid, O. S.; Abraham, N. L.; Abramowicz, H.; Abreu, H.; Abreu, R.; Abulaiti, Y.; Acharya, B. S.; Adachi, S.; Adamczyk, L.; Adelman, J.; Adersberger, M.; Adye, T.; Affolder, A. A.; Afik, Y.; Agatonovic-Jovin, T.; Agheorghiesei, C.; Aguilar-Saavedra, J. A.; Ahlen, S. P.; Ahmadov, F.; Aielli, G.; Akatsuka, S.; Akerstedt, H.; Åkesson, T. P. A.; Akilli, E.; Akimov, A. V.; Alberghi, G. L.; Albert, J.; Albicocco, P.; Alconada Verzini, M. J.; Alderweireldt, S. C.; Aleksa, M.; Aleksandrov, I. N.; Alexa, C.; Alexander, G.; Alexopoulos, T.; Alhroob, M.; Ali, B.; Aliev, M.; Alimonti, G.; Alison, J.; Alkire, S. P.; Allbrooke, B. M. M.; Allen, B. W.; Allport, P. P.; Aloisio, A.; Alonso, A.; Alonso, F.; Alpigiani, C.; Alshehri, A. A.; Alstaty, M. I.; Alvarez Gonzalez, B.; Álvarez Piqueras, D.; Alviggi, M. G.; Amadio, B. T.; Amaral Coutinho, Y.; Amelung, C.; Amidei, D.; Amor Dos Santos, S. P.; Amoroso, S.; Amundsen, G.; Anastopoulos, C.; Ancu, L. S.; Andari, N.; Andeen, T.; Anders, C. F.; Anders, J. K.; Anderson, K. J.; Andreazza, A.; Andrei, V.; Angelidakis, S.; Angelozzi, I.; Angerami, A.; Anisenkov, A. V.; Anjos, N.; Annovi, A.; Antel, C.; Antonelli, M.; Antonov, A.; Antrim, D. J.; Anulli, F.; Aoki, M.; Aperio Bella, L.; Arabidze, G.; Arai, Y.; Araque, J. P.; Araujo Ferraz, V.; Arce, A. T. H.; Ardell, R. E.; Arduh, F. A.; Arguin, J.-F.; Argyropoulos, S.; Arik, M.; Armbruster, A. J.; Armitage, L. J.; Arnaez, O.; Arnold, H.; Arratia, M.; Arslan, O.; Artamonov, A.; Artoni, G.; Artz, S.; Asai, S.; Asbah, N.; Ashkenazi, A.; Asquith, L.; Assamagan, K.; Astalos, R.; Atkinson, M.; Atlay, N. B.; Augsten, K.; Avolio, G.; Axen, B.; Ayoub, M. K.; Azuelos, G.; Baas, A. E.; Baca, M. J.; Bachacou, H.; Bachas, K.; Backes, M.; Bagnaia, P.; Bahmani, M.; Bahrasemani, H.; Baines, J. T.; Bajic, M.; Baker, O. K.; Baldin, E. M.; Balek, P.; Balli, F.; Balunas, W. K.; Banas, E.; Bandyopadhyay, A.; Banerjee, Sw.; Bannoura, A. A. E.; Barak, L.; Barberio, E. L.; Barberis, D.; Barbero, M.; Barillari, T.; Barisits, M.-S.; Barkeloo, J. T.; Barklow, T.; Barlow, N.; Barnes, S. L.; Barnett, B. M.; Barnett, R. M.; Barnovska-Blenessy, Z.; Baroncelli, A.; Barone, G.; Barr, A. J.; Barranco Navarro, L.; Barreiro, F.; Barreiro Guimarães da Costa, J.; Bartoldus, R.; Barton, A. E.; Bartos, P.; Basalaev, A.; Bassalat, A.; Bates, R. L.; Batista, S. J.; Batley, J. R.; Battaglia, M.; Bauce, M.; Bauer, F.; Bawa, H. S.; Beacham, J. B.; Beattie, M. D.; Beau, T.; Beauchemin, P. H.; Bechtle, P.; Beck, H. P.; Beck, H. C.; Becker, K.; Becker, M.; Becot, C.; Beddall, A. J.; Beddall, A.; Bednyakov, V. A.; Bedognetti, M.; Bee, C. P.; Beermann, T. A.; Begalli, M.; Begel, M.; Behr, J. K.; Bell, A. S.; Bella, G.; Bellagamba, L.; Bellerive, A.; Bellomo, M.; Belotskiy, K.; Beltramello, O.; Belyaev, N. L.; Benary, O.; Benchekroun, D.; Bender, M.; Bendtz, K.; Benekos, N.; Benhammou, Y.; Benhar Noccioli, E.; Benitez, J.; Benjamin, D. P.; Benoit, M.; Bensinger, J. R.; Bentvelsen, S.; Beresford, L.; Beretta, M.; Berge, D.; Bergeaas Kuutmann, E.; Berger, N.; Beringer, J.; Berlendis, S.; Bernard, N. R.; Bernardi, G.; Bernius, C.; Bernlochner, F. U.; Berry, T.; Berta, P.; Bertella, C.; Bertoli, G.; Bertolucci, F.; Bertram, I. A.; Bertsche, C.; Bertsche, D.; Besjes, G. J.; Bessidskaia Bylund, O.; Bessner, M.; Besson, N.; Betancourt, C.; Bethani, A.; Bethke, S.; Bevan, A. J.; Beyer, J.; Bianchi, R. M.; Biebel, O.; Biedermann, D.; Bielski, R.; Bierwagen, K.; Biesuz, N. V.; Biglietti, M.; Billoud, T. R. V.; Bilokon, H.; Bindi, M.; Bingul, A.; Bini, C.; Biondi, S.; Bisanz, T.; Bittrich, C.; Bjergaard, D. M.; Black, J. E.; Black, K. M.; Blair, R. E.; Blazek, T.; Bloch, I.; Blocker, C.; Blue, A.; Blum, W.; Blumenschein, U.; Blunier, S.; Bobbink, G. J.; Bobrovnikov, V. S.; Bocchetta, S. S.; Bocci, A.; Bock, C.; Boehler, M.; Boerner, D.; Bogavac, D.; Bogdanchikov, A. G.; Bohm, C.; Boisvert, V.; Bokan, P.; Bold, T.; Boldyrev, A. S.; Bolz, A. E.; Bomben, M.; Bona, M.; Boonekamp, M.; Borisov, A.; Borissov, G.; Bortfeldt, J.; Bortoletto, D.; Bortolotto, V.; Boscherini, D.; Bosman, M.; Bossio Sola, J. D.; Boudreau, J.; Bouffard, J.; Bouhova-Thacker, E. V.; Boumediene, D.; Bourdarios, C.; Boutle, S. K.; Boveia, A.; Boyd, J.; Boyko, I. R.; Bracinik, J.; Brandt, A.; Brandt, G.; Brandt, O.; Bratzler, U.; Brau, B.; Brau, J. E.; Breaden Madden, W. D.; Brendlinger, K.; Brennan, A. J.; Brenner, L.; Brenner, R.; Bressler, S.; Briglin, D. L.; Bristow, T. M.; Britton, D.; Britzger, D.; Brochu, F. M.; Brock, I.; Brock, R.; Brooijmans, G.; Brooks, T.; Brooks, W. K.; Brosamer, J.; Brost, E.; Broughton, J. H.; Bruckman de Renstrom, P. A.; Bruncko, D.; Bruni, A.; Bruni, G.; Bruni, L. S.; Brunt, Bh; Bruschi, M.; Bruscino, N.; Bryant, P.; Bryngemark, L.; Buanes, T.; Buat, Q.; Buchholz, P.; Buckley, A. G.; Budagov, I. A.; Buehrer, F.; Bugge, M. K.; Bulekov, O.; Bullock, D.; Burch, T. J.; Burdin, S.; Burgard, C. D.; Burger, A. M.; Burghgrave, B.; Burka, K.; Burke, S.; Burmeister, I.; Burr, J. T. P.; Busato, E.; Büscher, D.; Büscher, V.; Bussey, P.; Butler, J. M.; Buttar, C. M.; Butterworth, J. M.; Butti, P.; Buttinger, W.; Buzatu, A.; Buzykaev, A. R.; Cabrera Urbán, S.; Caforio, D.; Cairo, V. M.; Cakir, O.; Calace, N.; Calafiura, P.; Calandri, A.; Calderini, G.; Calfayan, P.; Callea, G.; Caloba, L. P.; Calvente Lopez, S.; Calvet, D.; Calvet, S.; Calvet, T. P.; Camacho Toro, R.; Camarda, S.; Camarri, P.; Cameron, D.; Caminal Armadans, R.; Camincher, C.; Campana, S.; Campanelli, M.; Camplani, A.; Campoverde, A.; Canale, V.; Cano Bret, M.; Cantero, J.; Cao, T.; Capeans Garrido, M. D. M.; Caprini, I.; Caprini, M.; Capua, M.; Carbone, R. M.; Cardarelli, R.; Cardillo, F.; Carli, I.; Carli, T.; Carlino, G.; Carlson, B. T.; Carminati, L.; Carney, R. M. D.; Caron, S.; Carquin, E.; Carrá, S.; Carrillo-Montoya, G. D.; Casadei, D.; Casado, M. P.; Casolino, M.; Casper, D. W.; Castelijn, R.; Castillo Gimenez, V.; Castro, N. F.; Catinaccio, A.; Catmore, J. R.; Cattai, A.; Caudron, J.; Cavaliere, V.; Cavallaro, E.; Cavalli, D.; Cavalli-Sforza, M.; Cavasinni, V.; Celebi, E.; Ceradini, F.; Cerda Alberich, L.; Cerqueira, A. S.; Cerri, A.; Cerrito, L.; Cerutti, F.; Cervelli, A.; Cetin, S. A.; Chafaq, A.; Chakraborty, D.; Chan, S. K.; Chan, W. S.; Chan, Y. L.; Chang, P.; Chapman, J. D.; Charlton, D. G.; Chau, C. C.; Chavez Barajas, C. A.; Che, S.; Cheatham, S.; Chegwidden, A.; Chekanov, S.; Chekulaev, S. V.; Chelkov, G. A.; Chelstowska, M. A.; Chen, C.; Chen, H.; Chen, J.; Chen, S.; Chen, S.; Chen, X.; Chen, Y.; Cheng, H. C.; Cheng, H. J.; Cheplakov, A.; Cheremushkina, E.; Cherkaoui El Moursli, R.; Cheu, E.; Cheung, K.; Chevalier, L.; Chiarella, V.; Chiarelli, G.; Chiodini, G.; Chisholm, A. S.; Chitan, A.; Chiu, Y. H.; Chizhov, M. V.; Choi, K.; Chomont, A. R.; Chouridou, S.; Chow, Y. S.; Christodoulou, V.; Chu, M. C.; Chudoba, J.; Chuinard, A. J.; Chwastowski, J. J.; Chytka, L.; Ciftci, A. K.; Cinca, D.; Cindro, V.; Cioara, I. A.; Ciocca, C.; Ciocio, A.; Cirotto, F.; Citron, Z. H.; Citterio, M.; Ciubancan, M.; Clark, A.; Clark, B. L.; Clark, M. R.; Clark, P. J.; Clarke, R. N.; Clement, C.; Coadou, Y.; Cobal, M.; Coccaro, A.; Cochran, J.; Colasurdo, L.; Cole, B.; Colijn, A. P.; Collot, J.; Colombo, T.; Conde Muiño, P.; Coniavitis, E.; Connell, S. H.; Connelly, I. A.; Constantinescu, S.; Conti, G.; Conventi, F.; Cooke, M.; Cooper-Sarkar, A. M.; Cormier, F.; Cormier, K. J. R.; Corradi, M.; Corriveau, F.; Cortes-Gonzalez, A.; Cortiana, G.; Costa, G.; Costa, M. J.; Costanzo, D.; Cottin, G.; Cowan, G.; Cox, B. E.; Cranmer, K.; Crawley, S. J.; Creager, R. A.; Cree, G.; Crépé-Renaudin, S.; Crescioli, F.; Cribbs, W. A.; Cristinziani, M.; Croft, V.; Crosetti, G.; Cueto, A.; Cuhadar Donszelmann, T.; Cukierman, A. R.; Cummings, J.; Curatolo, M.; Cúth, J.; Czekierda, S.; Czodrowski, P.; D'Amen, G.; D'Auria, S.; D'Eramo, L.; D'Onofrio, M.; da Cunha Sargedas de Sousa, M. J.; da Via, C.; Dabrowski, W.; Dado, T.; Dai, T.; Dale, O.; Dallaire, F.; Dallapiccola, C.; Dam, M.; Dandoy, J. R.; Daneri, M. F.; Dang, N. P.; Daniells, A. C.; Dann, N. S.; Danninger, M.; Dano Hoffmann, M.; Dao, V.; Darbo, G.; Darmora, S.; Dassoulas, J.; Dattagupta, A.; Daubney, T.; Davey, W.; David, C.; Davidek, T.; Davis, D. R.; Davison, P.; Dawe, E.; Dawson, I.; de, K.; de Asmundis, R.; de Benedetti, A.; de Castro, S.; de Cecco, S.; de Groot, N.; de Jong, P.; de la Torre, H.; de Lorenzi, F.; de Maria, A.; de Pedis, D.; de Salvo, A.; de Sanctis, U.; de Santo, A.; de Vasconcelos Corga, K.; de Vivie de Regie, J. B.; Debbe, R.; Debenedetti, C.; Dedovich, D. V.; Dehghanian, N.; Deigaard, I.; Del Gaudio, M.; Del Peso, J.; Delgove, D.; Deliot, F.; Delitzsch, C. M.; Dell'Acqua, A.; Dell'Asta, L.; Dell'Orso, M.; Della Pietra, M.; Della Volpe, D.; Delmastro, M.; Delporte, C.; Delsart, P. A.; Demarco, D. A.; Demers, S.; Demichev, M.; Demilly, A.; Denisov, S. P.; Denysiuk, D.; Derendarz, D.; Derkaoui, J. E.; Derue, F.; Dervan, P.; Desch, K.; Deterre, C.; Dette, K.; Devesa, M. R.; Deviveiros, P. O.; Dewhurst, A.; Dhaliwal, S.; di Bello, F. A.; di Ciaccio, A.; di Ciaccio, L.; di Clemente, W. K.; di Donato, C.; di Girolamo, A.; di Girolamo, B.; di Micco, B.; di Nardo, R.; di Petrillo, K. F.; di Simone, A.; di Sipio, R.; di Valentino, D.; Diaconu, C.; Diamond, M.; Dias, F. A.; Diaz, M. A.; Diehl, E. B.; Dietrich, J.; Díez Cornell, S.; Dimitrievska, A.; Dingfelder, J.; Dita, P.; Dita, S.; Dittus, F.; Djama, F.; Djobava, T.; Djuvsland, J. I.; Do Vale, M. A. B.; Dobos, D.; Dobre, M.; Doglioni, C.; Dolejsi, J.; Dolezal, Z.; Donadelli, M.; Donati, S.; Dondero, P.; Donini, J.; Dopke, J.; Doria, A.; Dova, M. T.; Doyle, A. T.; Drechsler, E.; Dris, M.; Du, Y.; Duarte-Campderros, J.; Dubreuil, A.; Duchovni, E.; Duckeck, G.; Ducourthial, A.; Ducu, O. A.; Duda, D.; Dudarev, A.; Dudder, A. Chr.; Duffield, E. M.; Duflot, L.; Dührssen, M.; Dumancic, M.; Dumitriu, A. E.; Duncan, A. K.; Dunford, M.; Duran Yildiz, H.; Düren, M.; Durglishvili, A.; Duschinger, D.; Dutta, B.; Dyndal, M.; Dziedzic, B. S.; Eckardt, C.; Ecker, K. M.; Edgar, R. C.; Eifert, T.; Eigen, G.; Einsweiler, K.; Ekelof, T.; El Kacimi, M.; El Kosseifi, R.; Ellajosyula, V.; Ellert, M.; Elles, S.; Ellinghaus, F.; Elliot, A. A.; Ellis, N.; Elmsheuser, J.; Elsing, M.; Emeliyanov, D.; Enari, Y.; Endner, O. C.; Ennis, J. S.; Erdmann, J.; Ereditato, A.; Ernst, M.; Errede, S.; Escalier, M.; Escobar, C.; Esposito, B.; Estrada Pastor, O.; Etienvre, A. I.; Etzion, E.; Evans, H.; Ezhilov, A.; Ezzi, M.; Fabbri, F.; Fabbri, L.; Fabiani, V.; Facini, G.; Fakhrutdinov, R. M.; Falciano, S.; Falla, R. J.; Faltova, J.; Fang, Y.; Fanti, M.; Farbin, A.; Farilla, A.; Farina, C.; Farina, E. M.; Farooque, T.; Farrell, S.; Farrington, S. M.; Farthouat, P.; Fassi, F.; Fassnacht, P.; Fassouliotis, D.; Faucci Giannelli, M.; Favareto, A.; Fawcett, W. J.; Fayard, L.; Fedin, O. L.; Fedorko, W.; Feigl, S.; Feligioni, L.; Feng, C.; Feng, E. J.; Feng, H.; Fenton, M. J.; Fenyuk, A. B.; Feremenga, L.; Fernandez Martinez, P.; Fernandez Perez, S.; Ferrando, J.; Ferrari, A.; Ferrari, P.; Ferrari, R.; Ferreira de Lima, D. E.; Ferrer, A.; Ferrere, D.; Ferretti, C.; Fiedler, F.; Filipčič, A.; Filipuzzi, M.; Filthaut, F.; Fincke-Keeler, M.; Finelli, K. D.; Fiolhais, M. C. N.; Fiorini, L.; Fischer, A.; Fischer, C.; Fischer, J.; Fisher, W. C.; Flaschel, N.; Fleck, I.; Fleischmann, P.; Fletcher, R. R. M.; Flick, T.; Flierl, B. M.; Flores Castillo, L. R.; Flowerdew, M. J.; Forcolin, G. T.; Formica, A.; Förster, F. A.; Forti, A.; Foster, A. G.; Fournier, D.; Fox, H.; Fracchia, S.; Francavilla, P.; Franchini, M.; Franchino, S.; Francis, D.; Franconi, L.; Franklin, M.; Frate, M.; Fraternali, M.; Freeborn, D.; Fressard-Batraneanu, S. M.; Freund, B.; Froidevaux, D.; Frost, J. A.; Fukunaga, C.; Fusayasu, T.; Fuster, J.; Gabaldon, C.; Gabizon, O.; Gabrielli, A.; Gabrielli, A.; Gach, G. P.; Gadatsch, S.; Gadomski, S.; Gagliardi, G.; Gagnon, L. G.; Galea, C.; Galhardo, B.; Gallas, E. J.; Gallop, B. J.; Gallus, P.; Galster, G.; Gan, K. K.; Ganguly, S.; Gao, Y.; Gao, Y. S.; Garay Walls, F. M.; García, C.; García Navarro, J. E.; García Pascual, J. A.; Garcia-Sciveres, M.; Gardner, R. W.; Garelli, N.; Garonne, V.; Gascon Bravo, A.; Gasnikova, K.; Gatti, C.; Gaudiello, A.; Gaudio, G.; Gavrilenko, I. L.; Gay, C.; Gaycken, G.; Gazis, E. N.; Gee, C. N. P.; Geisen, J.; Geisen, M.; Geisler, M. P.; Gellerstedt, K.; Gemme, C.; Genest, M. H.; Geng, C.; Gentile, S.; Gentsos, C.; George, S.; Gerbaudo, D.; Gershon, A.; Geßner, G.; Ghasemi, S.; Ghneimat, M.; Giacobbe, B.; Giagu, S.; Giangiacomi, N.; Giannetti, P.; Gibson, S. M.; Gignac, M.; Gilchriese, M.; Gillberg, D.; Gilles, G.; Gingrich, D. M.; Giordani, M. P.; Giorgi, F. M.; Giraud, P. F.; Giromini, P.; Giugliarelli, G.; Giugni, D.; Giuli, F.; Giuliani, C.; Giulini, M.; Gjelsten, B. K.; Gkaitatzis, S.; Gkialas, I.; Gkougkousis, E. L.; Gkountoumis, P.; Gladilin, L. K.; Glasman, C.; Glatzer, J.; Glaysher, P. C. F.; Glazov, A.; Goblirsch-Kolb, M.; Godlewski, J.; Goldfarb, S.; Golling, T.; Golubkov, D.; Gomes, A.; Gonçalo, R.; Goncalves Gama, R.; Goncalves Pinto Firmino da Costa, J.; Gonella, G.; Gonella, L.; Gongadze, A.; González de La Hoz, S.; Gonzalez-Sevilla, S.; Goossens, L.; Gorbounov, P. A.; Gordon, H. A.; Gorelov, I.; Gorini, B.; Gorini, E.; Gorišek, A.; Goshaw, A. T.; Gössling, C.; Gostkin, M. I.; Gottardo, C. A.; Goudet, C. R.; Goujdami, D.; Goussiou, A. G.; Govender, N.; Gozani, E.; Graber, L.; Grabowska-Bold, I.; Gradin, P. O. J.; Gramling, J.; Gramstad, E.; Grancagnolo, S.; Gratchev, V.; Gravila, P. M.; Gray, C.; Gray, H. M.; Greenwood, Z. D.; Grefe, C.; Gregersen, K.; Gregor, I. M.; Grenier, P.; Grevtsov, K.; Griffiths, J.; Grillo, A. A.; Grimm, K.; Grinstein, S.; Gris, Ph.; Grivaz, J.-F.; Groh, S.; Gross, E.; Grosse-Knetter, J.; Grossi, G. C.; Grout, Z. J.; Grummer, A.; Guan, L.; Guan, W.; Guenther, J.; Guescini, F.; Guest, D.; Gueta, O.; Gui, B.; Guido, E.; Guillemin, T.; Guindon, S.; Gul, U.; Gumpert, C.; Guo, J.; Guo, W.; Guo, Y.; Gupta, R.; Gupta, S.; Gustavino, G.; Gutelman, B. J.; Gutierrez, P.; Gutierrez Ortiz, N. G.; Gutschow, C.; Guyot, C.; Guzik, M. P.; Gwenlan, C.; Gwilliam, C. B.; Haas, A.; Haber, C.; Hadavand, H. K.; Haddad, N.; Hadef, A.; Hageböck, S.; Hagihara, M.; Hakobyan, H.; Haleem, M.; Haley, J.; Halladjian, G.; Hallewell, G. D.; Hamacher, K.; Hamal, P.; Hamano, K.; Hamilton, A.; Hamity, G. N.; Hamnett, P. G.; Han, L.; Han, S.; Hanagaki, K.; Hanawa, K.; Hance, M.; Haney, B.; Hanke, P.; Hansen, J. B.; Hansen, J. D.; Hansen, M. C.; Hansen, P. H.; Hara, K.; Hard, A. S.; Harenberg, T.; Hariri, F.; Harkusha, S.; Harrington, R. D.; Harrison, P. F.; Hartmann, N. M.; Hasegawa, Y.; Hasib, A.; Hassani, S.; Haug, S.; Hauser, R.; Hauswald, L.; Havener, L. B.; Havranek, M.; Hawkes, C. M.; Hawkings, R. J.; Hayakawa, D.; Hayden, D.; Hays, C. P.; Hays, J. M.; Hayward, H. S.; Haywood, S. J.; Head, S. J.; Heck, T.; Hedberg, V.; Heelan, L.; Heer, S.; Heidegger, K. K.; Heim, S.; Heim, T.; Heinemann, B.; Heinrich, J. J.; Heinrich, L.; Heinz, C.; Hejbal, J.; Helary, L.; Held, A.; Hellman, S.; Helsens, C.; Henderson, R. C. W.; Heng, Y.; Henkelmann, S.; Henriques Correia, A. M.; Henrot-Versille, S.; Herbert, G. H.; Herde, H.; Herget, V.; Hernández Jiménez, Y.; Herr, H.; Herten, G.; Hertenberger, R.; Hervas, L.; Herwig, T. C.; Hesketh, G. G.; Hessey, N. P.; Hetherly, J. W.; Higashino, S.; Higón-Rodriguez, E.; Hildebrand, K.; Hill, E.; Hill, J. C.; Hiller, K. H.; Hillier, S. J.; Hils, M.; Hinchliffe, I.; Hirose, M.; Hirschbuehl, D.; Hiti, B.; Hladik, O.; Hoad, X.; Hobbs, J.; Hod, N.; Hodgkinson, M. C.; Hodgson, P.; Hoecker, A.; Hoeferkamp, M. R.; Hoenig, F.; Hohn, D.; Holmes, T. R.; Homann, M.; Honda, S.; Honda, T.; Hong, T. M.; Hooberman, B. H.; Hopkins, W. H.; Horii, Y.; Horton, A. J.; Hostachy, J.-Y.; Hou, S.; Hoummada, A.; Howarth, J.; Hoya, J.; Hrabovsky, M.; Hrdinka, J.; Hristova, I.; Hrivnac, J.; Hryn'ova, T.; Hrynevich, A.; Hsu, P. J.; Hsu, S.-C.; Hu, Q.; Hu, S.; Huang, Y.; Hubacek, Z.; Hubaut, F.; Huegging, F.; Huffman, T. B.; Hughes, E. W.; Hughes, G.; Huhtinen, M.; Huo, P.; Huseynov, N.; Huston, J.; Huth, J.; Iacobucci, G.; Iakovidis, G.; Ibragimov, I.; Iconomidou-Fayard, L.; Idrissi, Z.; Iengo, P.; Igonkina, O.; Iizawa, T.; Ikegami, Y.; Ikeno, M.; Ilchenko, Y.; Iliadis, D.; Ilic, N.; Introzzi, G.; Ioannou, P.; Iodice, M.; Iordanidou, K.; Ippolito, V.; Isacson, M. F.; Ishijima, N.; Ishino, M.; Ishitsuka, M.; Issever, C.; Istin, S.; Ito, F.; Iturbe Ponce, J. M.; Iuppa, R.; Iwasaki, H.; Izen, J. M.; Izzo, V.; Jabbar, S.; Jackson, P.; Jacobs, R. M.; Jain, V.; Jakobi, K. B.; Jakobs, K.; Jakobsen, S.; Jakoubek, T.; Jamin, D. O.; Jana, D. K.; Jansky, R.; Janssen, J.; Janus, M.; Janus, P. A.; Jarlskog, G.; Javadov, N.; Javå¯Rek, T.; Javurkova, M.; Jeanneau, F.; Jeanty, L.; Jejelava, J.; Jelinskas, A.; Jenni, P.; Jeske, C.; Jézéquel, S.; Ji, H.; Jia, J.; Jiang, H.; Jiang, Y.; Jiang, Z.; Jiggins, S.; Jimenez Pena, J.; Jin, S.; Jinaru, A.; Jinnouchi, O.; Jivan, H.; Johansson, P.; Johns, K. A.; Johnson, C. A.; Johnson, W. J.; Jon-And, K.; Jones, R. W. L.; Jones, S. D.; Jones, S.; Jones, T. J.; Jongmanns, J.; Jorge, P. M.; Jovicevic, J.; Ju, X.; Juste Rozas, A.; Köhler, M. K.; Kaczmarska, A.; Kado, M.; Kagan, H.; Kagan, M.; Kahn, S. J.; Kaji, T.; Kajomovitz, E.; Kalderon, C. W.; Kaluza, A.; Kama, S.; Kamenshchikov, A.; Kanaya, N.; Kanjir, L.; Kantserov, V. A.; Kanzaki, J.; Kaplan, B.; Kaplan, L. S.; Kar, D.; Karakostas, K.; Karastathis, N.; Kareem, M. J.; Karentzos, E.; Karpov, S. N.; Karpova, Z. M.; Karthik, K.; Kartvelishvili, V.; Karyukhin, A. N.; Kasahara, K.; Kashif, L.; Kass, R. D.; Kastanas, A.; Kataoka, Y.; Kato, C.; Katre, A.; Katzy, J.; Kawade, K.; Kawagoe, K.; Kawamoto, T.; Kawamura, G.; Kay, E. F.; Kazanin, V. F.; Keeler, R.; Kehoe, R.; Keller, J. S.; Kellermann, E.; Kempster, J. J.; Kendrick, J.; Keoshkerian, H.; Kepka, O.; Kerševan, B. P.; Kersten, S.; Keyes, R. A.; Khader, M.; Khalil-Zada, F.; Khanov, A.; Kharlamov, A. G.; Kharlamova, T.; Khodinov, A.; Khoo, T. J.; Khovanskiy, V.; Khramov, E.; Khubua, J.; Kido, S.; Kilby, C. R.; Kim, H. Y.; Kim, S. H.; Kim, Y. K.; Kimura, N.; Kind, O. M.; King, B. T.; Kirchmeier, D.; Kirk, J.; Kiryunin, A. E.; Kishimoto, T.; Kisielewska, D.; Kitali, V.; Kivernyk, O.; Kladiva, E.; Klapdor-Kleingrothaus, T.; Klein, M. H.; Klein, M.; Klein, U.; Kleinknecht, K.; Klimek, P.; Klimentov, A.; Klingenberg, R.; Klingl, T.; Klioutchnikova, T.; Kluge, E.-E.; Kluit, P.; Kluth, S.; Kneringer, E.; Knoops, E. B. F. G.; Knue, A.; Kobayashi, A.; Kobayashi, D.; Kobayashi, T.; Kobel, M.; Kocian, M.; Kodys, P.; Koffas, T.; Koffeman, E.; Köhler, N. M.; Koi, T.; Kolb, M.; Koletsou, I.; Komar, A. A.; Komori, Y.; Kondo, T.; Kondrashova, N.; Köneke, K.; König, A. C.; Kono, T.; Konoplich, R.; Konstantinidis, N.; Kopeliansky, R.; Koperny, S.; Kopp, A. K.; Korcyl, K.; Kordas, K.; Korn, A.; Korol, A. A.; Korolkov, I.; Korolkova, E. V.; Kortner, O.; Kortner, S.; Kosek, T.; Kostyukhin, V. V.; Kotwal, A.; Koulouris, A.; Kourkoumeli-Charalampidi, A.; Kourkoumelis, C.; Kourlitis, E.; Kouskoura, V.; Kowalewska, A. B.; Kowalewski, R.; Kowalski, T. Z.; Kozakai, C.; Kozanecki, W.; Kozhin, A. S.; Kramarenko, V. A.; Kramberger, G.; Krasnopevtsev, D.; Krasny, M. W.; Krasznahorkay, A.; Krauss, D.; Kremer, J. A.; Kretzschmar, J.; Kreutzfeldt, K.; Krieger, P.; Krizka, K.; Kroeninger, K.; Kroha, H.; Kroll, J.; Kroll, J.; Kroseberg, J.; Krstic, J.; Kruchonak, U.; Krüger, H.; Krumnack, N.; Kruse, M. C.; Kubota, T.; Kucuk, H.; Kuday, S.; Kuechler, J. T.; Kuehn, S.; Kugel, A.; Kuger, F.; Kuhl, T.; Kukhtin, V.; Kukla, R.; Kulchitsky, Y.; Kuleshov, S.; Kulinich, Y. P.; Kuna, M.; Kunigo, T.; Kupco, A.; Kupfer, T.; Kuprash, O.; Kurashige, H.; Kurchaninov, L. L.; Kurochkin, Y. A.; Kurth, M. G.; Kus, V.; Kuwertz, E. S.; Kuze, M.; Kvita, J.; Kwan, T.; Kyriazopoulos, D.; La Rosa, A.; La Rosa Navarro, J. L.; La Rotonda, L.; La Ruffa, F.; Lacasta, C.; Lacava, F.; Lacey, J.; Lacker, H.; Lacour, D.; Ladygin, E.; Lafaye, R.; Laforge, B.; Lagouri, T.; Lai, S.; Lammers, S.; Lampl, W.; Lançon, E.; Landgraf, U.; Landon, M. P. J.; Lanfermann, M. C.; Lang, V. S.; Lange, J. C.; Langenberg, R. J.; Lankford, A. J.; Lanni, F.; Lantzsch, K.; Lanza, A.; Lapertosa, A.; Laplace, S.; Laporte, J. F.; Lari, T.; Lasagni Manghi, F.; Lassnig, M.; Lau, T. S.; Laurelli, P.; Lavrijsen, W.; Law, A. T.; Laycock, P.; Lazovich, T.; Lazzaroni, M.; Le, B.; Le Dortz, O.; Le Guirriec, E.; Le Quilleuc, E. P.; Leblanc, M.; Lecompte, T.; Ledroit-Guillon, F.; Lee, C. A.; Lee, G. R.; Lee, S. C.; Lee, L.; Lefebvre, B.; Lefebvre, G.; Lefebvre, M.; Legger, F.; Leggett, C.; Lehmann Miotto, G.; Lei, X.; Leight, W. A.; Leite, M. A. L.; Leitner, R.; Lellouch, D.; Lemmer, B.; Leney, K. J. C.; Lenz, T.; Lenzi, B.; Leone, R.; Leone, S.; Leonidopoulos, C.; Lerner, G.; Leroy, C.; Lesage, A. A. J.; Lester, C. G.; Levchenko, M.; Levêque, J.; Levin, D.; Levinson, L. J.; Levy, M.; Lewis, D.; Li, B.; Li, Changqiao; Li, H.; Li, L.; Li, Q.; Li, Q.; Li, S.; Li, X.; Li, Y.; Liang, Z.; Liberti, B.; Liblong, A.; Lie, K.; Liebal, J.; Liebig, W.; Limosani, A.; Lin, S. C.; Lin, T. H.; Lindquist, B. E.; Lionti, A. E.; Lipeles, E.; Lipniacka, A.; Lisovyi, M.; Liss, T. M.; Lister, A.; Litke, A. M.; Liu, B.; Liu, H.; Liu, H.; Liu, J. K. K.; Liu, J.; Liu, J. B.; Liu, K.; Liu, L.; Liu, M.; Liu, Y. L.; Liu, Y.; Livan, M.; Lleres, A.; Llorente Merino, J.; Lloyd, S. L.; Lo, C. Y.; Lo Sterzo, F.; Lobodzinska, E. M.; Loch, P.; Loebinger, F. K.; Loesle, A.; Loew, K. M.; Loginov, A.; Lohse, T.; Lohwasser, K.; Lokajicek, M.; Long, B. A.; Long, J. D.; Long, R. E.; Longo, L.; Looper, K. A.; Lopez, J. A.; Lopez Mateos, D.; Lopez Paz, I.; Lopez Solis, A.; Lorenz, J.; Lorenzo Martinez, N.; Losada, M.; Lösel, P. J.; Lou, X.; Lounis, A.; Love, J.; Love, P. A.; Lu, H.; Lu, N.; Lu, Y. J.; Lubatti, H. J.; Luci, C.; Lucotte, A.; Luedtke, C.; Luehring, F.; Lukas, W.; Luminari, L.; Lundberg, O.; Lund-Jensen, B.; Lutz, M. S.; Luzi, P. M.; Lynn, D.; Lysak, R.; Lytken, E.; Lyu, F.; Lyubushkin, V.; Ma, H.; Ma, L. L.; Ma, Y.; Maccarrone, G.; Macchiolo, A.; MacDonald, C. M.; Maček, B.; Machado Miguens, J.; Madaffari, D.; Madar, R.; Mader, W. F.; Madsen, A.; Maeda, J.; Maeland, S.; Maeno, T.; Maevskiy, A. S.; Magerl, V.; Mahlstedt, J.; Maiani, C.; Maidantchik, C.; Maier, A. A.; Maier, T.; Maio, A.; Majersky, O.; Majewski, S.; Makida, Y.; Makovec, N.; Malaescu, B.; Malecki, Pa.; Maleev, V. P.; Malek, F.; Mallik, U.; Malon, D.; Malone, C.; Maltezos, S.; Malyukov, S.; Mamuzic, J.; Mancini, G.; Mandić, I.; Maneira, J.; Manhaes de Andrade Filho, L.; Manjarres Ramos, J.; Mankinen, K. H.; Mann, A.; Manousos, A.; Mansoulie, B.; Mansour, J. D.; Mantifel, R.; Mantoani, M.; Manzoni, S.; Mapelli, L.; Marceca, G.; March, L.; Marchese, L.; Marchiori, G.; Marcisovsky, M.; Marjanovic, M.; Marley, D. E.; Marroquim, F.; Marsden, S. P.; Marshall, Z.; Martensson, M. U. F.; Marti-Garcia, S.; Martin, C. B.; Martin, T. A.; Martin, V. J.; Martin Dit Latour, B.; Martinez, M.; Martinez Outschoorn, V. I.; Martin-Haugh, S.; Martoiu, V. S.; Martyniuk, A. C.; Marzin, A.; Masetti, L.; Mashimo, T.; Mashinistov, R.; Masik, J.; Maslennikov, A. L.; Massa, L.; Mastrandrea, P.; Mastroberardino, A.; Masubuchi, T.; Mättig, P.; Maurer, J.; Maxfield, S. J.; Maximov, D. A.; Mazini, R.; Maznas, I.; Mazza, S. M.; Mc Fadden, N. C.; Mc Goldrick, G.; Mc Kee, S. P.; McCarn, A.; McCarthy, R. L.; McCarthy, T. G.; McClymont, L. I.; McDonald, E. F.; McFayden, J. A.; McHedlidze, G.; McMahon, S. J.; McNamara, P. C.; McPherson, R. A.; Meehan, S.; Megy, T. J.; Mehlhase, S.; Mehta, A.; Meideck, T.; Meier, K.; Meirose, B.; Melini, D.; Mellado Garcia, B. R.; Mellenthin, J. D.; Melo, M.; Meloni, F.; Melzer, A.; Menary, S. B.; Meng, L.; Meng, X. T.; Mengarelli, A.; Menke, S.; Meoni, E.; Mergelmeyer, S.; Merlassino, C.; Mermod, P.; Merola, L.; Meroni, C.; Merritt, F. S.; Messina, A.; Metcalfe, J.; Mete, A. S.; Meyer, C.; Meyer, J.-P.; Meyer, J.; Meyer Zu Theenhausen, H.; Miano, F.; Middleton, R. P.; Miglioranzi, S.; Mijović, L.; Mikenberg, G.; Mikestikova, M.; Mikuž, M.; Milesi, M.; Milic, A.; Millar, D. A.; Miller, D. W.; Mills, C.; Milov, A.; Milstead, D. A.; Minaenko, A. A.; Minami, Y.; Minashvili, I. A.; Mincer, A. I.; Mindur, B.; Mineev, M.; Minegishi, Y.; Ming, Y.; Mir, L. M.; Mistry, K. P.; Mitani, T.; Mitrevski, J.; Mitsou, V. A.; Miucci, A.; Miyagawa, P. S.; Mizukami, A.; Mjörnmark, J. U.; Mkrtchyan, T.; Mlynarikova, M.; Moa, T.; Mochizuki, K.; Mogg, P.; Mohapatra, S.; Molander, S.; Moles-Valls, R.; Mondragon, M. C.; Mönig, K.; Monk, J.; Monnier, E.; Montalbano, A.; Montejo Berlingen, J.; Monticelli, F.; Monzani, S.; Moore, R. W.; Morange, N.; Moreno, D.; Moreno Llácer, M.; Morettini, P.; Morgenstern, S.; Mori, D.; Mori, T.; Morii, M.; Morinaga, M.; Morisbak, V.; Morley, A. K.; Mornacchi, G.; Morris, J. D.; Morvaj, L.; Moschovakos, P.; Mosidze, M.; Moss, H. J.; Moss, J.; Motohashi, K.; Mount, R.; Mountricha, E.; Moyse, E. J. W.; Muanza, S.; Mueller, F.; Mueller, J.; Mueller, R. S. P.; Muenstermann, D.; Mullen, P.; Mullier, G. A.; Munoz Sanchez, F. J.; Murray, W. J.; Musheghyan, H.; Muškinja, M.; Myagkov, A. G.; Myska, M.; Nachman, B. P.; Nackenhorst, O.; Nagai, K.; Nagai, R.; Nagano, K.; Nagasaka, Y.; Nagata, K.; Nagel, M.; Nagy, E.; Nairz, A. M.; Nakahama, Y.; Nakamura, K.; Nakamura, T.; Nakano, I.; Naranjo Garcia, R. F.; Narayan, R.; Narrias Villar, D. I.; Naryshkin, I.; Naumann, T.; Navarro, G.; Nayyar, R.; Neal, H. A.; Nechaeva, P. Yu.; Neep, T. J.; Negri, A.; Negrini, M.; Nektarijevic, S.; Nellist, C.; Nelson, A.; Nelson, M. E.; Nemecek, S.; Nemethy, P.; Nessi, M.; Neubauer, M. S.; Neumann, M.; Newman, P. R.; Ng, T. Y.; Nguyen Manh, T.; Nickerson, R. B.; Nicolaidou, R.; Nielsen, J.; Nikolaenko, V.; Nikolic-Audit, I.; Nikolopoulos, K.; Nilsen, J. K.; Nilsson, P.; Ninomiya, Y.; Nisati, A.; Nishu, N.; Nisius, R.; Nitsche, I.; Nitta, T.; Nobe, T.; Noguchi, Y.; Nomachi, M.; Nomidis, I.; Nomura, M. A.; Nooney, T.; Nordberg, M.; Norjoharuddeen, N.; Novgorodova, O.; Nowak, S.; Nozaki, M.; Nozka, L.; Ntekas, K.; Nurse, E.; Nuti, F.; O'Connor, K.; O'Neil, D. C.; O'Rourke, A. A.; O'Shea, V.; Oakham, F. G.; Oberlack, H.; Obermann, T.; Ocariz, J.; Ochi, A.; Ochoa, I.; Ochoa-Ricoux, J. P.; Oda, S.; Odaka, S.; Oh, A.; Oh, S. H.; Ohm, C. C.; Ohman, H.; Oide, H.; Okawa, H.; Okumura, Y.; Okuyama, T.; Olariu, A.; Oleiro Seabra, L. F.; Olivares Pino, S. A.; Oliveira Damazio, D.; Olszewski, A.; Olszowska, J.; Onofre, A.; Onogi, K.; Onyisi, P. U. E.; Oppen, H.; Oreglia, M. J.; Oren, Y.; Orestano, D.; Orlando, N.; Orr, R. S.; Osculati, B.; Ospanov, R.; Otero Y Garzon, G.; Otono, H.; Ouchrif, M.; Ould-Saada, F.; Ouraou, A.; Oussoren, K. P.; Ouyang, Q.; Owen, M.; Owen, R. E.; Ozcan, V. E.; Ozturk, N.; Pachal, K.; Pacheco Pages, A.; Pacheco Rodriguez, L.; Padilla Aranda, C.; Pagan Griso, S.; Paganini, M.; Paige, F.; Palacino, G.; Palazzo, S.; Palestini, S.; Palka, M.; Pallin, D.; Panagiotopoulou, E. St.; Panagoulias, I.; Pandini, C. E.; Panduro Vazquez, J. G.; Pani, P.; Panitkin, S.; Pantea, D.; Paolozzi, L.; Papadopoulou, Th. D.; Papageorgiou, K.; Paramonov, A.; Paredes Hernandez, D.; Parker, A. J.; Parker, M. A.; Parker, K. A.; Parodi, F.; Parsons, J. A.; Parzefall, U.; Pascuzzi, V. R.; Pasner, J. M.; Pasqualucci, E.; Passaggio, S.; Pastore, Fr.; Pataraia, S.; Pater, J. R.; Pauly, T.; Pearson, B.; Pedraza Lopez, S.; Pedro, R.; Peleganchuk, S. V.; Penc, O.; Peng, C.; Peng, H.; Penwell, J.; Peralva, B. S.; Perego, M. M.; Perepelitsa, D. V.; Peri, F.; Perini, L.; Pernegger, H.; Perrella, S.; Peschke, R.; Peshekhonov, V. D.; Peters, K.; Peters, R. F. Y.; Petersen, B. A.; Petersen, T. C.; Petit, E.; Petridis, A.; Petridou, C.; Petroff, P.; Petrolo, E.; Petrov, M.; Petrucci, F.; Pettersson, N. E.; Peyaud, A.; Pezoa, R.; Phillips, F. H.; Phillips, P. W.; Piacquadio, G.; Pianori, E.; Picazio, A.; Piccaro, E.; Pickering, M. A.; Piegaia, R.; Pilcher, J. E.; Pilkington, A. D.; Pin, A. W. J.; Pinamonti, M.; Pinfold, J. L.; Pirumov, H.; Pitt, M.; Plazak, L.; Pleier, M.-A.; Pleskot, V.; Plotnikova, E.; Pluth, D.; Podberezko, P.; Poettgen, R.; Poggi, R.; Poggioli, L.; Pogrebnyak, I.; Pohl, D.; Polesello, G.; Poley, A.; Policicchio, A.; Polifka, R.; Polini, A.; Pollard, C. S.; Polychronakos, V.; Pommès, K.; Ponomarenko, D.; Pontecorvo, L.; Popeneciu, G. A.; Pospisil, S.; Potamianos, K.; Potrap, I. N.; Potter, C. J.; Poulsen, T.; Poveda, J.; Pozo Astigarraga, M. E.; Pralavorio, P.; Pranko, A.; Prell, S.; Price, D.; Primavera, M.; Prince, S.; Proklova, N.; Prokofiev, K.; Prokoshin, F.; Protopopescu, S.; Proudfoot, J.; Przybycien, M.; Puri, A.; Puzo, P.; Qian, J.; Qin, G.; Qin, Y.; Quadt, A.; Queitsch-Maitland, M.; Quilty, D.; Raddum, S.; Radeka, V.; Radescu, V.; Radhakrishnan, S. K.; Radloff, P.; Rados, P.; Ragusa, F.; Rahal, G.; Raine, J. A.; Rajagopalan, S.; Rangel-Smith, C.; Rashid, T.; Raspopov, S.; Ratti, M. G.; Rauch, D. M.; Rauscher, F.; Rave, S.; Ravinovich, I.; Rawling, J. H.; Raymond, M.; Read, A. L.; Readioff, N. P.; Reale, M.; Rebuzzi, D. M.; Redelbach, A.; Redlinger, G.; Reece, R.; Reed, R. G.; Reeves, K.; Rehnisch, L.; Reichert, J.; Reiss, A.; Rembser, C.; Ren, H.; Rescigno, M.; Resconi, S.; Resseguie, E. D.; Rettie, S.; Reynolds, E.; Rezanova, O. L.; Reznicek, P.; Rezvani, R.; Richter, R.; Richter, S.; Richter-Was, E.; Ricken, O.; Ridel, M.; Rieck, P.; Riegel, C. J.; Rieger, J.; Rifki, O.; Rijssenbeek, M.; Rimoldi, A.; Rimoldi, M.; Rinaldi, L.; Ripellino, G.; Ristić, B.; Ritsch, E.; Riu, I.; Rizatdinova, F.; Rizvi, E.; Rizzi, C.; Roberts, R. T.; Robertson, S. H.; Robichaud-Veronneau, A.; Robinson, D.; Robinson, J. E. M.; Robson, A.; Rocco, E.; Roda, C.; Rodina, Y.; Rodriguez Bosca, S.; Rodriguez Perez, A.; Rodriguez Rodriguez, D.; Roe, S.; Rogan, C. S.; Røhne, O.; Roloff, J.; Romaniouk, A.; Romano, M.; Romano Saez, S. M.; Romero Adam, E.; Rompotis, N.; Ronzani, M.; Roos, L.; Rosati, S.; Rosbach, K.; Rose, P.; Rosien, N.-A.; Rossi, E.; Rossi, L. P.; Rosten, J. H. N.; Rosten, R.; Rotaru, M.; Rothberg, J.; Rousseau, D.; Rozanov, A.; Rozen, Y.; Ruan, X.; Rubbo, F.; Rühr, F.; Ruiz-Martinez, A.; Rurikova, Z.; Rusakovich, N. A.; Russell, H. L.; Rutherfoord, J. P.; Ruthmann, N.; Ryabov, Y. F.; Rybar, M.; Rybkin, G.; Ryu, S.; Ryzhov, A.; Rzehorz, G. F.; Saavedra, A. F.; Sabato, G.; Sacerdoti, S.; Sadrozinski, H. F.-W.; Sadykov, R.; Safai Tehrani, F.; Saha, P.; Sahinsoy, M.; Saimpert, M.; Saito, M.; Saito, T.; Sakamoto, H.; Sakurai, Y.; Salamanna, G.; Salazar Loyola, J. E.; Salek, D.; Sales de Bruin, P. H.; Salihagic, D.; Salnikov, A.; Salt, J.; Salvatore, D.; Salvatore, F.; Salvucci, A.; Salzburger, A.; Sammel, D.; Sampsonidis, D.; Sampsonidou, D.; Sánchez, J.; Sanchez Martinez, V.; Sanchez Pineda, A.; Sandaker, H.; Sandbach, R. L.; Sander, C. O.; Sandhoff, M.; Sandoval, C.; Sankey, D. P. C.; Sannino, M.; Sano, Y.; Sansoni, A.; Santoni, C.; Santos, H.; Santoyo Castillo, I.; Sapronov, A.; Saraiva, J. G.; Sarrazin, B.; Sasaki, O.; Sato, K.; Sauvan, E.; Savage, G.; Savard, P.; Savic, N.; Sawyer, C.; Sawyer, L.; Saxon, J.; Sbarra, C.; Sbrizzi, A.; Scanlon, T.; Scannicchio, D. A.; Schaarschmidt, J.; Schacht, P.; Schachtner, B. M.; Schaefer, D.; Schaefer, L.; Schaefer, R.; Schaeffer, J.; Schaepe, S.; Schaetzel, S.; Schäfer, U.; Schaffer, A. C.; Schaile, D.; Schamberger, R. D.; Schegelsky, V. A.; Scheirich, D.; Schernau, M.; Schiavi, C.; Schier, S.; Schildgen, L. K.; Schillo, C.; Schioppa, M.; Schlenker, S.; Schmidt-Sommerfeld, K. R.; Schmieden, K.; Schmitt, C.; Schmitt, S.; Schmitz, S.; Schnoor, U.; Schoeffel, L.; Schoening, A.; Schoenrock, B. D.; Schopf, E.; Schott, M.; Schouwenberg, J. F. P.; Schovancova, J.; Schramm, S.; Schuh, N.; Schulte, A.; Schultens, M. J.; Schultz-Coulon, H.-C.; Schulz, H.; Schumacher, M.; Schumm, B. A.; Schune, Ph.; Schwartzman, A.; Schwarz, T. A.; Schweiger, H.; Schwemling, Ph.; Schwienhorst, R.; Schwindling, J.; Sciandra, A.; Sciolla, G.; Scornajenghi, M.; Scuri, F.; Scutti, F.; Searcy, J.; Seema, P.; Seidel, S. C.; Seiden, A.; Seixas, J. M.; Sekhniaidze, G.; Sekhon, K.; Sekula, S. J.; Semprini-Cesari, N.; Senkin, S.; Serfon, C.; Serin, L.; Serkin, L.; Sessa, M.; Seuster, R.; Severini, H.; Sfiligoj, T.; Sforza, F.; Sfyrla, A.; Shabalina, E.; Shaikh, N. W.; Shan, L. Y.; Shang, R.; Shank, J. T.; Shapiro, M.; Shatalov, P. B.; Shaw, K.; Shaw, S. M.; Shcherbakova, A.; Shehu, C. Y.; Shen, Y.; Sherafati, N.; Sherwood, P.; Shi, L.; Shimizu, S.; Shimmin, C. O.; Shimojima, M.; Shipsey, I. P. J.; Shirabe, S.; Shiyakova, M.; Shlomi, J.; Shmeleva, A.; Shoaleh Saadi, D.; Shochet, M. J.; Shojaii, S.; Shope, D. R.; Shrestha, S.; Shulga, E.; Shupe, M. A.; Sicho, P.; Sickles, A. M.; Sidebo, P. E.; Sideras Haddad, E.; Sidiropoulou, O.; Sidoti, A.; Siegert, F.; Sijacki, Dj.; Silva, J.; Silverstein, S. B.; Simak, V.; Simic, Lj.; Simion, S.; Simioni, E.; Simmons, B.; Simon, M.; Sinervo, P.; Sinev, N. B.; Sioli, M.; Siragusa, G.; Siral, I.; Sivoklokov, S. Yu.; Sjölin, J.; Skinner, M. B.; Skubic, P.; Slater, M.; Slavicek, T.; Slawinska, M.; Sliwa, K.; Slovak, R.; Smakhtin, V.; Smart, B. H.; Smiesko, J.; Smirnov, N.; Smirnov, S. Yu.; Smirnov, Y.; Smirnova, L. N.; Smirnova, O.; Smith, J. W.; Smith, M. N. K.; Smith, R. W.; Smizanska, M.; Smolek, K.; Snesarev, A. A.; Snyder, I. M.; Snyder, S.; Sobie, R.; Socher, F.; Soffer, A.; Søgaard, A.; Soh, D. A.; Sokhrannyi, G.; Solans Sanchez, C. A.; Solar, M.; Soldatov, E. Yu.; Soldevila, U.; Solodkov, A. A.; Soloshenko, A.; Solovyanov, O. V.; Solovyev, V.; Sommer, P.; Son, H.; Sopczak, A.; Sosa, D.; Sotiropoulou, C. L.; Soualah, R.; Soukharev, A. M.; South, D.; Sowden, B. C.; Spagnolo, S.; Spalla, M.; Spangenberg, M.; Spanò, F.; Sperlich, D.; Spettel, F.; Spieker, T. M.; Spighi, R.; Spigo, G.; Spiller, L. A.; Spousta, M.; St. Denis, R. D.; Stabile, A.; Stamen, R.; Stamm, S.; Stanecka, E.; Stanek, R. W.; Stanescu, C.; Stanitzki, M. M.; Stapf, B. S.; Stapnes, S.; Starchenko, E. A.; Stark, G. H.; Stark, J.; Stark, S. H.; Staroba, P.; Starovoitov, P.; Stärz, S.; Staszewski, R.; Steinberg, P.; Stelzer, B.; Stelzer, H. J.; Stelzer-Chilton, O.; Stenzel, H.; Stewart, G. A.; Stockton, M. C.; Stoebe, M.; Stoicea, G.; Stolte, P.; Stonjek, S.; Stradling, A. R.; Straessner, A.; Stramaglia, M. E.; Strandberg, J.; Strandberg, S.; Strauss, M.; Strizenec, P.; Ströhmer, R.; Strom, D. M.; Stroynowski, R.; Strubig, A.; Stucci, S. A.; Stugu, B.; Styles, N. A.; Su, D.; Su, J.; Suchek, S.; Sugaya, Y.; Suk, M.; Sulin, V. V.; Sultan, Dms; Sultansoy, S.; Sumida, T.; Sun, S.; Sun, X.; Suruliz, K.; Suster, C. J. E.; Sutton, M. R.; Suzuki, S.; Svatos, M.; Swiatlowski, M.; Swift, S. P.; Sykora, I.; Sykora, T.; Ta, D.; Tackmann, K.; Taenzer, J.; Taffard, A.; Tafirout, R.; Tahirovic, E.; Taiblum, N.; Takai, H.; Takashima, R.; Takasugi, E. H.; Takeshita, T.; Takubo, Y.; Talby, M.; Talyshev, A. A.; Tanaka, J.; Tanaka, M.; Tanaka, R.; Tanaka, S.; Tanioka, R.; Tannenwald, B. B.; Tapia Araya, S.; Tapprogge, S.; Tarem, S.; Tartarelli, G. F.; Tas, P.; Tasevsky, M.; Tashiro, T.; Tassi, E.; Tavares Delgado, A.; Tayalati, Y.; Taylor, A. C.; Taylor, A. J.; Taylor, G. N.; Taylor, P. T. E.; Taylor, W.; Teixeira-Dias, P.; Temple, D.; Ten Kate, H.; Teng, P. K.; Teoh, J. J.; Tepel, F.; Terada, S.; Terashi, K.; Terron, J.; Terzo, S.; Testa, M.; Teuscher, R. J.; Theveneaux-Pelzer, T.; Thiele, F.; Thomas, J. P.; Thomas-Wilsker, J.; Thompson, P. D.; Thompson, A. S.; Thomsen, L. A.; Thomson, E.; Tibbetts, M. J.; Ticse Torres, R. E.; Tikhomirov, V. O.; Tikhonov, Yu. A.; Timoshenko, S.; Tipton, P.; Tisserant, S.; Todome, K.; Todorova-Nova, S.; Todt, S.; Tojo, J.; Tokár, S.; Tokushuku, K.; Tolley, E.; Tomlinson, L.; Tomoto, M.; Tompkins, L.; Toms, K.; Tong, B.; Tornambe, P.; Torrence, E.; Torres, H.; Torró Pastor, E.; Toth, J.; Touchard, F.; Tovey, D. R.; Treado, C. J.; Trefzger, T.; Tresoldi, F.; Tricoli, A.; Trigger, I. M.; Trincaz-Duvoid, S.; Tripiana, M. F.; Trischuk, W.; Trocmé, B.; Trofymov, A.; Troncon, C.; Trottier-McDonald, M.; Trovatelli, M.; Truong, L.; Trzebinski, M.; Trzupek, A.; Tsang, K. W.; Tseng, J. C.-L.; Tsiareshka, P. V.; Tsipolitis, G.; Tsirintanis, N.; Tsiskaridze, S.; Tsiskaridze, V.; Tskhadadze, E. G.; Tsui, K. M.; Tsukerman, I. I.; Tsulaia, V.; Tsuno, S.; Tsybychev, D.; Tu, Y.; Tudorache, A.; Tudorache, V.; Tulbure, T. T.; Tuna, A. N.; Tupputi, S. A.; Turchikhin, S.; Turgeman, D.; Turk Cakir, I.; Turra, R.; Tuts, P. M.; Ucchielli, G.; Ueda, I.; Ughetto, M.; Ukegawa, F.; Unal, G.; Undrus, A.; Unel, G.; Ungaro, F. C.; Unno, Y.; Unverdorben, C.; Urban, J.; Urquijo, P.; Urrejola, P.; Usai, G.; Usui, J.; Vacavant, L.; Vacek, V.; Vachon, B.; Vadla, K. O. H.; Vaidya, A.; Valderanis, C.; Valdes Santurio, E.; Valente, M.; Valentinetti, S.; Valero, A.; Valéry, L.; Valkar, S.; Vallier, A.; Valls Ferrer, J. A.; van den Wollenberg, W.; van der Graaf, H.; van Gemmeren, P.; van Nieuwkoop, J.; van Vulpen, I.; van Woerden, M. C.; Vanadia, M.; Vandelli, W.; Vaniachine, A.; Vankov, P.; Vardanyan, G.; Vari, R.; Varnes, E. W.; Varni, C.; Varol, T.; Varouchas, D.; Vartapetian, A.; Varvell, K. E.; Vasquez, J. G.; Vasquez, G. A.; Vazeille, F.; Vazquez Schroeder, T.; Veatch, J.; Veeraraghavan, V.; Veloce, L. M.; Veloso, F.; Veneziano, S.; Ventura, A.; Venturi, M.; Venturi, N.; Venturini, A.; Vercesi, V.; Verducci, M.; Verkerke, W.; Vermeulen, A. T.; Vermeulen, J. C.; Vetterli, M. C.; Viaux Maira, N.; Viazlo, O.; Vichou, I.; Vickey, T.; Vickey Boeriu, O. E.; Viehhauser, G. H. A.; Viel, S.; Vigani, L.; Villa, M.; Villaplana Perez, M.; Vilucchi, E.; Vincter, M. G.; Vinogradov, V. B.; Vishwakarma, A.; Vittori, C.; Vivarelli, I.; Vlachos, S.; Vogel, M.; Vokac, P.; Volpi, G.; von der Schmitt, H.; von Toerne, E.; Vorobel, V.; Vorobev, K.; Vos, M.; Voss, R.; Vossebeld, J. H.; Vranjes, N.; Vranjes Milosavljevic, M.; Vrba, V.; Vreeswijk, M.; Vuillermet, R.; Vukotic, I.; Wagner, P.; Wagner, W.; Wagner-Kuhr, J.; Wahlberg, H.; Wahrmund, S.; Walder, J.; Walker, R.; Walkowiak, W.; Wallangen, V.; Wang, C.; Wang, C.; Wang, F.; Wang, H.; Wang, H.; Wang, J.; Wang, J.; Wang, Q.; Wang, R.; Wang, S. M.; Wang, T.; Wang, W.; Wang, W.; Wang, Z.; Wanotayaroj, C.; Warburton, A.; Ward, C. P.; Wardrope, D. R.; Washbrook, A.; Watkins, P. M.; Watson, A. T.; Watson, M. F.; Watts, G.; Watts, S.; Waugh, B. M.; Webb, A. F.; Webb, S.; Weber, M. S.; Weber, S. W.; Weber, S. A.; Webster, J. S.; Weidberg, A. R.; Weinert, B.; Weingarten, J.; Weirich, M.; Weiser, C.; Weits, H.; Wells, P. S.; Wenaus, T.; Wengler, T.; Wenig, S.; Wermes, N.; Werner, M. D.; Werner, P.; Wessels, M.; Weston, T. D.; Whalen, K.; Whallon, N. L.; Wharton, A. M.; White, A. S.; White, A.; White, M. J.; White, R.; Whiteson, D.; Whitmore, B. W.; Wickens, F. J.; Wiedenmann, W.; Wielers, M.; Wiglesworth, C.; Wiik-Fuchs, L. A. M.; Wildauer, A.; Wilk, F.; Wilkens, H. G.; Williams, H. H.; Williams, S.; Willis, C.; Willocq, S.; Wilson, J. A.; Wingerter-Seez, I.; Winkels, E.; Winklmeier, F.; Winston, O. J.; Winter, B. T.; Wittgen, M.; Wobisch, M.; Wolf, T. M. H.; Wolff, R.; Wolter, M. W.; Wolters, H.; Wong, V. W. S.; Worm, S. D.; Wosiek, B. K.; Wotschack, J.; Wozniak, K. W.; Wu, M.; Wu, S. L.; Wu, X.; Wu, Y.; Wyatt, T. R.; Wynne, B. M.; Xella, S.; Xi, Z.; Xia, L.; Xu, D.; Xu, L.; Xu, T.; Yabsley, B.; Yacoob, S.; Yamaguchi, D.; Yamaguchi, Y.; Yamamoto, A.; Yamamoto, S.; Yamanaka, T.; Yamane, F.; Yamatani, M.; Yamazaki, Y.; Yan, Z.; Yang, H.; Yang, H.; Yang, Y.; Yang, Z.; Yao, W.-M.; Yap, Y. C.; Yasu, Y.; Yatsenko, E.; Yau Wong, K. H.; Ye, J.; Ye, S.; Yeletskikh, I.; Yigitbasi, E.; Yildirim, E.; Yorita, K.; Yoshihara, K.; Young, C.; Young, C. J. S.; Yu, J.; Yu, J.; Yuen, S. P. Y.; Yusuff, I.; Zabinski, B.; Zacharis, G.; Zaidan, R.; Zaitsev, A. M.; Zakharchuk, N.; Zalieckas, J.; Zaman, A.; Zambito, S.; Zanzi, D.; Zeitnitz, C.; Zemaityte, G.; Zemla, A.; Zeng, J. C.; Zeng, Q.; Zenin, O.; Ženiš, T.; Zerwas, D.; Zhang, D.; Zhang, F.; Zhang, G.; Zhang, H.; Zhang, J.; Zhang, L.; Zhang, L.; Zhang, M.; Zhang, P.; Zhang, R.; Zhang, R.; Zhang, X.; Zhang, Y.; Zhang, Z.; Zhao, X.; Zhao, Y.; Zhao, Z.; Zhemchugov, A.; Zhou, B.; Zhou, C.; Zhou, L.; Zhou, M.; Zhou, M.; Zhou, N.; Zhu, C. G.; Zhu, H.; Zhu, J.; Zhu, Y.; Zhuang, X.; Zhukov, K.; Zibell, A.; Zieminska, D.; Zimine, N. I.; Zimmermann, C.; Zimmermann, S.; Zinonos, Z.; Zinser, M.; Ziolkowski, M.; Živković, L.; Zobernig, G.; Zoccoli, A.; Zou, R.; Zur Nedden, M.; Zwalinski, L.; Atlas Collaboration

2017-11-01

The analysis of the momentum difference between charged hadrons in high-energy proton-proton collisions is performed in order to study coherent particle production. The observed correlation pattern agrees with a model of a helical QCD string fragmenting into a chain of ground-state hadrons. A threshold momentum difference in the production of adjacent pairs of charged hadrons is observed, in agreement with model predictions. The presence of low-mass hadron chains also explains the emergence of charge-combination-dependent two-particle correlations commonly attributed to Bose-Einstein interference. The data sample consists of 190 μ b-1 of minimum-bias events collected with proton-proton collisions at a center-of-mass energy √{s }=7 TeV in the early low-luminosity data taking with the ATLAS detector at the LHC.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aaboud, M.; Aad, G.; Abbott, B.

The analysis of the momentum difference between charged hadrons in high-energy proton-proton collisions is performed in order to study coherent particle production. The observed correlation pattern agrees with a model of a helical QCD string fragmenting into a chain of ground-state hadrons. A threshold momentum difference in the production of adjacent pairs of charged hadrons is observed, in agreement with model predictions. The presence of low-mass hadron chains also explains the emergence of charge-combination-dependent two-particle correlations commonly attributed to Bose-Einstein interference. Here, the data sample consists of 190 μb –1 of minimum-bias events collected with proton-proton collisions at a center-of-massmore » energy √s=7 TeV in the early low-luminosity data taking with the ATLAS detector at the LHC.« less

NLO QCD corrections to tt-barbb-bar production at the LHC: 1. quark-antiquark annihilation

NASA Astrophysics Data System (ADS)

Bredenstein, A.; Denner, A.; Dittmaier, S.; Pozzorini, S.

2008-08-01

The process pp → tt-barbb-bar + X represents a very important background reaction to searches at the LHC, in particular to tt-barH production where the Higgs boson decays into a bb-bar pair. A successful analysis of tt-barH at the LHC requires the knowledge of direct tt-barbb-bar production at next-to-leading order in QCD. We take the first step in this direction upon calculating the next-to-leading-order QCD corrections to the subprocess initiated by qbar q annihilation. We devote an appendix to the general issue of rational terms resulting from ultraviolet or infrared (soft or collinear) singularities within dimensional regularization. There we show that, for arbitrary processes, in the Feynman gauge, rational terms of infrared origin cancel in truncated one-loop diagrams and result only from trivial self-energy corrections.

Predictions for diphoton production at the LHC through NNLO in QCD

DOE PAGES

Campbell, John M.; Ellis, R. Keith; Li, Ye; ...

2016-07-29

In this paper we present a next-to-next-to-leading order (NNLO) calculation of the processmore » $$pp\\rightarrow \\gamma\\gamma$$ that we have implemented into the parton level Monte Carlo code MCFM. We do not find agreement with the previous calculation of this process in the literature. In addition to the $$\\mathcal{O}(\\alpha_s^2)$$ corrections present at NNLO, we include some effects arising at $$\\mathcal{O}(\\alpha_s^3)$$, namely those associated with gluon-initiated closed fermion loops. We investigate the role of this process in the context of studies of QCD at colliders and as a background for searches for new physics, paying particular attention to the diphoton invariant mass spectrum. We demonstrate that the NNLO QCD prediction for the shape of this spectrum agrees well with functional forms used in recent data-driven fits.« less

Structural features of the DNA hairpin d(ATCCTA-GTTA-TAGGAT): formation of a G-A base pair in the loop.

PubMed Central

van Dongen, M J; Mooren, M M; Willems, E F; van der Marel, G A; van Boom, J H; Wijmenga, S S; Hilbers, C W

1997-01-01

The three-dimensional structure of the hairpin formed by d(ATCCTA-GTTA-TAGGAT) has been determined by means of two-dimensional NMR studies, distance geometry and molecular dynamics calculations. The first and the last residues of the tetraloop of this hairpin form a sheared G-A base pair on top of the six Watson-Crick base pairs in the stem. The glycosidic torsion angles of the guanine and adenine residues in the G-A base pair reside in the anti and high- anti domain ( approximately -60 degrees ) respectively. Several dihedral angles in the loop adopt non-standard values to accommodate this base pair. The first and second residue in the loop are stacked in a more or less normal helical fashion; the fourth loop residue also stacks upon the stem, while the third residue is directed away from the loop region. The loop structure can be classified as a so-called type-I loop, in which the bases at the 5'-end of the loop stack in a continuous fashion. In this situation, loop stability is unlikely to depend heavily on the nature of the unpaired bases in the loop. Moreover, the present study indicates that the influence of the polarity of a closing A.T pair is much less significant than that of a closing C.G base pair. PMID:9092659

A four-way junction with triple-helical arms: design, characterization, and stability.

PubMed

Makube, N; Klump, H H

2000-05-01

The formation of the four-way junction containing four triple-helical arms has been demonstrated using chemical methods (polyacrylamide gel electrophoresis and chemical footprinting using OsO(4) as a probe) and physical methods (UV absorbance melting and DSC). The junction J(T1T3) was assembled from two 20-mer purine strands and two 44-mer pyrimidine strands. To determine the contribution of the different arms to the stability of the complete structure of J(T1T3), the junction was compared to two simplified substructures, J(T1) and J(T3), respectively. Common to these complexes is the underlying double-helical four-way junction Js. Addition of Na(+) had a profound effect on stabilizing and subsequently folding the junctions into the stacked X-structures. The following results support the structure present: (i) The native polyacrylamide electrophoresis exhibits only a single band(s) corresponding to one species present when all four single strands are mixed in equal amounts. (ii) OsO(4) modifications were investigated at pH 5.0 and in the presence of 10 mM Mg(2+) and 100 mM Na(+). There is no cleavage of thymine residues at the branch point and throughout the structure. (iii) The thermal unfolding of J(T1) and J(T3) illustrates that the triple-helical arms are more stable than the double-helical arms which are contained in these junctions and that J(T1T3) with four triple-helical arms is slightly more stable than J(T1) and J(T3). (iv) The calorimetric transition enthalpies determined for the arms of J(T1T3) are comparable to those associated with the unfolding of its corresponding arms in J(T1) and J(T3). The results also illustrate that the formation of the junctions is not restricted by the pH, [Na(+)], sequence composition of the arms, and/or the loop position. Copyright 2000 Academic Press.

Worldline approach to helicity flip in plane waves

NASA Astrophysics Data System (ADS)

Ilderton, Anton; Torgrimsson, Greger

2016-04-01

We apply worldline methods to the study of vacuum polarization effects in plane wave backgrounds, in both scalar and spinor QED. We calculate helicity-flip probabilities to one loop order and treated exactly in the background field, and provide a toolkit of methods for use in investigations of higher-order processes. We also discuss the connections between the worldline, S-matrix, and lightfront approaches to vacuum polarization effects.

QCD Coupling from a Nonperturbative Determination of the Three-Flavor Λ Parameter

DOE PAGES

Bruno, Mattia; Brida, Mattia Dalla; Fritzsch, Patrick; ...

2017-09-08

We present a lattice determination of the Λ parameter in three-flavor QCD and the strong coupling at the Z pole mass. Computing the nonperturbative running of the coupling in the range from 0.2 to 70 GeV, and using experimental input values for the masses and decay constants of the pion and the kaon, we obtain Λ(3)MS=341(12) MeV. The nonperturbative running up to very high energies guarantees that systematic effects associated with perturbation theory are well under control. Using the four-loop prediction for Λ(5)MS/Λ(3)MS yields α(5)MS(mZ)=0.11852(84).

Zimmermann's forest formula, infrared divergences and the QCD beta function

NASA Astrophysics Data System (ADS)

Herzog, Franz

2018-01-01

We review Zimmermann's forest formula, which solves Bogoliubov's recursive R-operation for the subtraction of ultraviolet divergences in perturbative Quantum Field Theory. We further discuss a generalisation of the R-operation which subtracts besides ultraviolet also Euclidean infrared divergences. This generalisation, which goes under the name of the R*-operation, can be used efficiently to compute renormalisation constants. We will discuss several results obtained by this method with focus on the QCD beta function at five loops as well as the application to hadronic Higgs boson decay rates at N4LO. This article summarizes a talk given at the Wolfhart Zimmermann Memorial Symposium.

Corrections beyond the leading order in π{sup 0} → e{sup +}e{sup −} process

DOE Office of Scientific and Technical Information (OSTI.GOV)

Husek, T.; Kampf, K.; Novotný, J.

2016-01-22

We briefly summarize experimental and theoretical results on the rare decay π{sup 0} → e{sup +}e{sup −}. Two-loop QED corrections are reviewed and the bremsstrahlung contribution beyond the soft-photon approximation is analytically calculated. Using the leading logarithm approximation, the possible contribution of QCD corrections is estimated. The complete result can be used to fit the value of the contact interaction coupling χ{sup (r)} to the recent KTeV experiment with the result χ{sup (r)}(M{sub ρ}) = 4.5±1.0.

Next-to-leading order γ γ + 2 - jet production at the LHC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bern, Z.; Dixon, L. J.; Febres Cordero, F.

We present next-to-leading-order QCD predictions for cross sections and for a comprehensive set of distributions in γγ+2-jet production at the Large Hadron Collider. We consider the contributions from loop amplitudes for two photons and four gluons, but we neglect top quarks. We use BlackHat together with SHERPA to carry out the computation. We use a Frixione cone isolation for the photons. We study standard sets of cuts on the jets and the photons and also sets of cuts appropriate for studying backgrounds to Higgs-boson production via vector-boson fusion.

Gluon-fusion Higgs production in the Standard Model Effective Field Theory

NASA Astrophysics Data System (ADS)

Deutschmann, Nicolas; Duhr, Claude; Maltoni, Fabio; Vryonidou, Eleni

2017-12-01

We provide the complete set of predictions needed to achieve NLO accuracy in the Standard Model Effective Field Theory at dimension six for Higgs production in gluon fusion. In particular, we compute for the first time the contribution of the chromomagnetic operator {\\overline{Q}}_LΦ σ {q}_RG at NLO in QCD, which entails two-loop virtual and one-loop real contributions, as well as renormalisation and mixing with the Yukawa operator {Φ}^{\\dagger}Φ{\\overline{Q}}_LΦ {q}_R and the gluon-fusion operator Φ†Φ GG. Focusing on the top-quark-Higgs couplings, we consider the phenomenological impact of the NLO corrections in constraining the three relevant operators by implementing the results into the M adG raph5_ aMC@NLO frame-work. This allows us to compute total cross sections as well as to perform event generation at NLO that can be directly employed in experimental analyses.

Energy and helicity of magnetic torus knots and braids

NASA Astrophysics Data System (ADS)

Oberti, Chiara; Ricca, Renzo L.

2018-02-01

By considering steady magnetic fields in the shape of torus knots and unknots in ideal magnetohydrodynamics, we compute some fundamental geometric and physical properties to provide estimates for magnetic energy and helicity. By making use of an appropriate parametrization, we show that knots with dominant toroidal coils that are a good model for solar coronal loops have negligible total torsion contribution to magnetic helicity while writhing number provides a good proxy. Hence, by the algebraic definition of writhe based on crossing numbers, we show that the estimated values of writhe based on image analysis provide reliable information for the exact values of helicity. We also show that magnetic energy is linearly related to helicity, and the effect of the confinement of magnetic field can be expressed in terms of geometric information. These results can find useful application in solar and plasma physics, where braided structures are often present.

Two-color QCD at high density

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boz, Tamer; Skullerud, Jon-Ivar; Centre for the Subatomic Structure of Matter, Adelaide University, Adelaide, SA 5005

2016-01-22

QCD at high chemical potential has interesting properties such as deconfinement of quarks. Two-color QCD, which enables numerical simulations on the lattice, constitutes a laboratory to study QCD at high chemical potential. Among the interesting properties of two-color QCD at high density is the diquark condensation, for which we present recent results obtained on a finer lattice compared to previous studies. The quark propagator in two-color QCD at non-zero chemical potential is referred to as the Gor’kov propagator. We express the Gor’kov propagator in terms of form factors and present recent lattice simulation results.

STAND, a class of P-loop NTPases including animal and plant regulators of programmed cell death: multiple, complex domain architectures, unusual phyletic patterns, and evolution by horizontal gene transfer.

PubMed

Leipe, Detlef D; Koonin, Eugene V; Aravind, L

2004-10-08

Using sequence profile analysis and sequence-based structure predictions, we define a previously unrecognized, widespread class of P-loop NTPases. The signal transduction ATPases with numerous domains (STAND) class includes the AP-ATPases (animal apoptosis regulators CED4/Apaf-1, plant disease resistance proteins, and bacterial AfsR-like transcription regulators) and NACHT NTPases (e.g. NAIP, TLP1, Het-E-1) that have been studied extensively in the context of apoptosis, pathogen response in animals and plants, and transcriptional regulation in bacteria. We show that, in addition to these well-characterized protein families, the STAND class includes several other groups of (predicted) NTPase domains from diverse signaling and transcription regulatory proteins from bacteria and eukaryotes, and three Archaea-specific families. We identified the STAND domain in several biologically well-characterized proteins that have not been suspected to have NTPase activity, including soluble adenylyl cyclases, nephrocystin 3 (implicated in polycystic kidney disease), and Rolling pebble (a regulator of muscle development); these findings are expected to facilitate elucidation of the functions of these proteins. The STAND class belongs to the additional strand, catalytic E division of P-loop NTPases together with the AAA+ ATPases, RecA/helicase-related ATPases, ABC-ATPases, and VirD4/PilT-like ATPases. The STAND proteins are distinguished from other P-loop NTPases by the presence of unique sequence motifs associated with the N-terminal helix and the core strand-4, as well as a C-terminal helical bundle that is fused to the NTPase domain. This helical module contains a signature GxP motif in the loop between the two distal helices. With the exception of the archaeal families, almost all STAND NTPases are multidomain proteins containing three or more domains. In addition to the NTPase domain, these proteins typically contain DNA-binding or protein-binding domains, superstructure-forming repeats, such as WD40 and TPR, and enzymatic domains involved in signal transduction, including adenylate cyclases and kinases. By analogy to the AAA+ ATPases, it can be predicted that STAND NTPases use the C-terminal helical bundle as a "lever" to transmit the conformational changes brought about by NTP hydrolysis to effector domains. STAND NTPases represent a novel paradigm in signal transduction, whereby adaptor, regulatory switch, scaffolding, and, in some cases, signal-generating moieties are combined into a single polypeptide. The STAND class consists of 14 distinct families, and the evolutionary history of most of these families is riddled with dramatic instances of lineage-specific expansion and apparent horizontal gene transfer. The STAND NTPases are most abundant in developmentally and organizationally complex prokaryotes and eukaryotes. Transfer of genes for STAND NTPases from bacteria to eukaryotes on several occasions might have played a significant role in the evolution of eukaryotic signaling systems.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wemmer, D.E.; Kumar, N.V.; Metrione, R.M.

Toxin II from Radianthus paumotensis (Rp/sub II/) has been investigated by high-resolution NMR and chemical sequencing methods. Resonance assignments have been obtained for this protein by the sequential approach. NMR assignments could not be made consistent with the previously reported primary sequence for this protein, and chemical methods have been used to determine a sequence with which the NMR data are consistent. Analysis of the 2D NOE spectra shows that the protein secondary structure is comprised of two sequences of ..beta..-sheet, probably joined into a distorted continuous sheet, connected by turns and extended loops, without any regular ..cap alpha..-helical segments.more » The residues previously implicated in activity in this class of proteins, D8 and R13, occur in a loop region.« less

High thermodynamic stability of parametrically designed helical bundles

DOE PAGES

Huang, Po -Ssu; Oberdorfer, Gustav; Xu, Chunfu; ...

2014-10-24

Here we describe a procedure for designing proteins with backbones produced by varying the parameters in the Crick coiled coil–generating equations. Combinatorial design calculations identify low-energy sequences for alternative helix supercoil arrangements, and the helices in the lowest-energy arrangements are connected by loop building. We design an antiparallel monomeric untwisted three-helix bundle with 80-residue helices, an antiparallel monomeric right-handed four-helix bundle, and a pentameric parallel left-handed five-helix bundle. The designed proteins are extremely stable (extrapolated ΔG fold > 60 kilocalories per mole), and their crystal structures are close to those of the design models with nearly identical core packing betweenmore » the helices. The approach enables the custom design of hyperstable proteins with fine-tuned geometries for a wide range of applications.« less

Viscous-enstrophy scaling law for Navier-Stokes reconnection

NASA Astrophysics Data System (ADS)

Kerr, Robert M.

2017-11-01

Simulations of perturbed, helical trefoil vortex knots and anti-parallel vortices find ν-independent collapse of temporally scaled (√{ ν} Z) - 1 / 2, Z enstrophy, between when the loops first touch at tΓ, and when reconnection ends at tx for the viscosity ν varying by 256. Due to mathematical bounds upon higher-order norms, this collapse requires that the domain increase as ν decreases, possibly to allow large-scale negative helicity to grow as compensation for small-scale positive helicity and enstrophy growth. This mechanism could be a step towards explaining how smooth solutions of the Navier-Stokes can generate finite-energy dissipation in a finite time as ν -> 0 .

Cascade unlooping of a low-pitch helical spring under tension

NASA Astrophysics Data System (ADS)

Starostin, E. L.; van der Heijden, G. H. M.

2009-06-01

We study the force vs. extension behaviour of a helical spring made of a thin torsionally stiff anisotropic elastic rod. Our focus is on springs of very low helical pitch. For certain parameters of the problem such a spring is found not to unwind when pulled but rather to form hockles that pop out one by one and lead to a highly non-monotonic force-extension curve. Between abrupt loop pop-outs this curve is well described by the planar elastica whose relevant solutions are classified. Our results may be relevant for tightly coiled nanosprings in future micro- and nano(electro)mechanical devices.

Measurement of the parity-violating asymmetry parameter αb and the helicity amplitudes for the decay Λb0→J/ψΛ0 with the ATLAS detector

NASA Astrophysics Data System (ADS)

Aad, G.; Abajyan, T.; Abbott, B.; Abdallah, J.; Abdel Khalek, S.; Abdinov, O.; Aben, R.; Abi, B.; Abolins, M.; Abouzeid, O. S.; Abramowicz, H.; Abreu, H.; Abulaiti, Y.; Acharya, B. S.; Adamczyk, L.; Adams, D. L.; Adelman, J.; Adomeit, S.; Adye, T.; Agatonovic-Jovin, T.; Aguilar-Saavedra, J. A.; Agustoni, M.; Ahlen, S. P.; Ahmad, A.; Ahmadov, F.; Aielli, G.; Åkesson, T. P. A.; Akimoto, G.; Akimov, A. V.; Albert, J.; Albrand, S.; Alconada Verzini, M. J.; Aleksa, M.; Aleksandrov, I. N.; Alexa, C.; Alexander, G.; Alexandre, G.; Alexopoulos, T.; Alhroob, M.; Alimonti, G.; Alio, L.; Alison, J.; Allbrooke, B. M. M.; Allison, L. J.; Allport, P. P.; Allwood-Spiers, S. E.; Almond, J.; Aloisio, A.; Alon, R.; Alonso, A.; Alonso, F.; Alpigiani, C.; Altheimer, A.; Alvarez Gonzalez, B.; Alviggi, M. G.; Amako, K.; Amaral Coutinho, Y.; Amelung, C.; Amidei, D.; Ammosov, V. V.; Amor Dos Santos, S. P.; Amorim, A.; Amoroso, S.; Amram, N.; Amundsen, G.; Anastopoulos, C.; Ancu, L. S.; Andari, N.; Andeen, T.; Anders, C. F.; Anders, G.; Anderson, K. J.; Andreazza, A.; Andrei, V.; Anduaga, X. S.; Angelidakis, S.; Anger, P.; Angerami, A.; Anghinolfi, F.; Anisenkov, A. V.; Anjos, N.; Annovi, A.; Antonaki, A.; Antonelli, M.; Antonov, A.; Antos, J.; Anulli, F.; Aoki, M.; Aperio Bella, L.; Apolle, R.; Arabidze, G.; Aracena, I.; Arai, Y.; Araque, J. P.; Arce, A. T. H.; Arguin, J.-F.; Argyropoulos, S.; Arik, M.; Armbruster, A. J.; Arnaez, O.; Arnal, V.; Arslan, O.; Artamonov, A.; Artoni, G.; Asai, S.; Asbah, N.; Ashkenazi, A.; Ask, S.; Åsman, B.; Asquith, L.; Assamagan, K.; Astalos, R.; Atkinson, M.; Atlay, N. B.; Auerbach, B.; Auge, E.; Augsten, K.; Aurousseau, M.; Avolio, G.; Azuelos, G.; Azuma, Y.; Baak, M. A.; Bacci, C.; Bachacou, H.; Bachas, K.; Backes, M.; Backhaus, M.; Backus Mayes, J.; Badescu, E.; Bagiacchi, P.; Bagnaia, P.; Bai, Y.; Bailey, D. C.; Bain, T.; Baines, J. T.; Baker, O. K.; Baker, S.; Balek, P.; Balli, F.; Banas, E.; Banerjee, Sw.; Banfi, D.; Bangert, A.; Bannoura, A. A. E.; Bansal, V.; Bansil, H. S.; Barak, L.; Baranov, S. P.; Barber, T.; Barberio, E. L.; Barberis, D.; Barbero, M.; Barillari, T.; Barisonzi, M.; Barklow, T.; Barlow, N.; Barnett, B. M.; Barnett, R. M.; Barnovska, Z.; Baroncelli, A.; Barone, G.; Barr, A. J.; Barreiro, F.; Barreiro Guimarães da Costa, J.; Bartoldus, R.; Barton, A. E.; Bartos, P.; Bartsch, V.; Bassalat, A.; Basye, A.; Bates, R. L.; Batkova, L.; Batley, J. R.; Battistin, M.; Bauer, F.; Bawa, H. S.; Beau, T.; Beauchemin, P. H.; Beccherle, R.; Bechtle, P.; Beck, H. P.; Becker, K.; Becker, S.; Beckingham, M.; Becot, C.; Beddall, A. J.; Beddall, A.; Bedikian, S.; Bednyakov, V. A.; Bee, C. P.; Beemster, L. J.; Beermann, T. A.; Begel, M.; Behr, K.; Belanger-Champagne, C.; Bell, P. J.; Bell, W. H.; Bella, G.; Bellagamba, L.; Bellerive, A.; Bellomo, M.; Belloni, A.; Beloborodova, O. L.; Belotskiy, K.; Beltramello, O.; Benary, O.; Benchekroun, D.; Bendtz, K.; Benekos, N.; Benhammou, Y.; Benhar Noccioli, E.; Benitez Garcia, J. A.; Benjamin, D. P.; Bensinger, J. R.; Benslama, K.; Bentvelsen, S.; Berge, D.; Bergeaas Kuutmann, E.; Berger, N.; Berghaus, F.; Berglund, E.; Beringer, J.; Bernard, C.; Bernat, P.; Bernius, C.; Bernlochner, F. U.; Berry, T.; Berta, P.; Bertella, C.; Bertolucci, F.; Besana, M. I.; Besjes, G. J.; Bessidskaia, O.; Besson, N.; Betancourt, C.; Bethke, S.; Bhimji, W.; Bianchi, R. M.; Bianchini, L.; Bianco, M.; Biebel, O.; Bieniek, S. P.; Bierwagen, K.; Biesiada, J.; Biglietti, M.; Bilbao de Mendizabal, J.; Bilokon, H.; Bindi, M.; Binet, S.; Bingul, A.; Bini, C.; Black, C. W.; Black, J. E.; Black, K. M.; Blackburn, D.; Blair, R. E.; Blanchard, J.-B.; Blazek, T.; Bloch, I.; Blocker, C.; Blum, W.; Blumenschein, U.; Bobbink, G. J.; Bobrovnikov, V. S.; Bocchetta, S. S.; Bocci, A.; Boddy, C. R.; Boehler, M.; Boek, J.; Boek, T. T.; Bogaerts, J. A.; Bogdanchikov, A. G.; Bogouch, A.; Bohm, C.; Bohm, J.; Boisvert, V.; Bold, T.; Boldea, V.; Boldyrev, A. S.; Bolnet, N. M.; Bomben, M.; Bona, M.; Boonekamp, M.; Borisov, A.; Borissov, G.; Borri, M.; Borroni, S.; Bortfeldt, J.; Bortolotto, V.; Bos, K.; Boscherini, D.; Bosman, M.; Boterenbrood, H.; Boudreau, J.; Bouffard, J.; Bouhova-Thacker, E. V.; Boumediene, D.; Bourdarios, C.; Bousson, N.; Boutouil, S.; Boveia, A.; Boyd, J.; Boyko, I. R.; Bozovic-Jelisavcic, I.; Bracinik, J.; Branchini, P.; Brandt, A.; Brandt, G.; Brandt, O.; Bratzler, U.; Brau, B.; Brau, J. E.; Braun, H. M.; Brazzale, S. F.; Brelier, B.; Brendlinger, K.; Brennan, A. J.; Brenner, R.; Bressler, S.; Bristow, K.; Bristow, T. M.; Britton, D.; Brochu, F. M.; Brock, I.; Brock, R.; Bromberg, C.; Bronner, J.; Brooijmans, G.; Brooks, T.; Brooks, W. K.; Brosamer, J.; Brost, E.; Brown, G.; Brown, J.; Bruckman de Renstrom, P. A.; Bruncko, D.; Bruneliere, R.; Brunet, S.; Bruni, A.; Bruni, G.; Bruschi, M.; Bryngemark, L.; Buanes, T.; Buat, Q.; Bucci, F.; Buchholz, P.; Buckingham, R. M.; Buckley, A. G.; Buda, S. I.; Budagov, I. A.; Buehrer, F.; Bugge, L.; Bugge, M. K.; Bulekov, O.; Bundock, A. C.; Burckhart, H.; Burdin, S.; Burghgrave, B.; Burke, S.; Burmeister, I.; Busato, E.; Büscher, V.; Bussey, P.; Buszello, C. P.; Butler, B.; Butler, J. M.; Butt, A. I.; Buttar, C. M.; Butterworth, J. M.; Butti, P.; Buttinger, W.; Buzatu, A.; Byszewski, M.; Cabrera Urbán, S.; Caforio, D.; Cakir, O.; Calafiura, P.; Calderini, G.; Calfayan, P.; Calkins, R.; Caloba, L. P.; Calvet, D.; Calvet, S.; Camacho Toro, R.; Camarda, S.; Cameron, D.; Caminada, L. M.; Caminal Armadans, R.; Campana, S.; Campanelli, M.; Campoverde, A.; Canale, V.; Canepa, A.; Cantero, J.; Cantrill, R.; Cao, T.; Capeans Garrido, M. D. M.; Caprini, I.; Caprini, M.; Capua, M.; Caputo, R.; Cardarelli, R.; Carli, T.; Carlino, G.; Carminati, L.; Caron, S.; Carquin, E.; Carrillo-Montoya, G. D.; Carter, A. A.; Carter, J. R.; Carvalho, J.; Casadei, D.; Casado, M. P.; Castaneda-Miranda, E.; Castelli, A.; Castillo Gimenez, V.; Castro, N. F.; Catastini, P.; Catinaccio, A.; Catmore, J. R.; Cattai, A.; Cattani, G.; Caughron, S.; Cavaliere, V.; Cavalli, D.; Cavalli-Sforza, M.; Cavasinni, V.; Ceradini, F.; Cerio, B.; Cerny, K.; Cerqueira, A. S.; Cerri, A.; Cerrito, L.; Cerutti, F.; Cerv, M.; Cervelli, A.; Cetin, S. A.; Chafaq, A.; Chakraborty, D.; Chalupkova, I.; Chan, K.; Chang, P.; Chapleau, B.; Chapman, J. D.; Charfeddine, D.; Charlton, D. G.; Chau, C. C.; Chavez Barajas, C. A.; Cheatham, S.; Chegwidden, A.; Chekanov, S.; Chekulaev, S. V.; Chelkov, G. A.; Chelstowska, M. A.; Chen, C.; Chen, H.; Chen, K.; Chen, L.; Chen, S.; Chen, X.; Chen, Y.; Cheng, H. C.; Cheng, Y.; Cheplakov, A.; Cherkaoui El Moursli, R.; Chernyatin, V.; Cheu, E.; Chevalier, L.; Chiarella, V.; Chiefari, G.; Childers, J. T.; Chilingarov, A.; Chiodini, G.; Chisholm, A. S.; Chislett, R. T.; Chitan, A.; Chizhov, M. V.; Chouridou, S.; Chow, B. K. B.; Christidi, I. A.; Chromek-Burckhart, D.; Chu, M. L.; Chudoba, J.; Chytka, L.; Ciapetti, G.; Ciftci, A. K.; Ciftci, R.; Cinca, D.; Cindro, V.; Ciocio, A.; Cirkovic, P.; Citron, Z. H.; Citterio, M.; Ciubancan, M.; Clark, A.; Clark, P. J.; Clarke, R. N.; Cleland, W.; Clemens, J. C.; Clement, B.; Clement, C.; Coadou, Y.; Cobal, M.; Coccaro, A.; Cochran, J.; Coffey, L.; Cogan, J. G.; Coggeshall, J.; Cole, B.; Cole, S.; Colijn, A. P.; Collins-Tooth, C.; Collot, J.; Colombo, T.; Colon, G.; Compostella, G.; Conde Muiño, P.; Coniavitis, E.; Conidi, M. C.; Connell, S. H.; Connelly, I. A.; Consonni, S. M.; Consorti, V.; Constantinescu, S.; Conta, C.; Conti, G.; Conventi, F.; Cooke, M.; Cooper, B. D.; Cooper-Sarkar, A. M.; Cooper-Smith, N. J.; Copic, K.; Cornelissen, T.; Corradi, M.; Corriveau, F.; Corso-Radu, A.; Cortes-Gonzalez, A.; Cortiana, G.; Costa, G.; Costa, M. J.; Costanzo, D.; Côté, D.; Cottin, G.; Cowan, G.; Cox, B. E.; Cranmer, K.; Cree, G.; Crépé-Renaudin, S.; Crescioli, F.; Crispin Ortuzar, M.; Cristinziani, M.; Crosetti, G.; Cuciuc, C.-M.; Cuenca Almenar, C.; Cuhadar Donszelmann, T.; Cummings, J.; Curatolo, M.; Cuthbert, C.; Czirr, H.; Czodrowski, P.; Czyczula, Z.; D'Auria, S.; D'Onofrio, M.; da Cunha Sargedas de Sousa, M. J.; da Via, C.; Dabrowski, W.; Dafinca, A.; Dai, T.; Dale, O.; Dallaire, F.; Dallapiccola, C.; Dam, M.; Daniells, A. C.; Dano Hoffmann, M.; Dao, V.; Darbo, G.; Darlea, G. L.; Darmora, S.; Dassoulas, J. A.; Davey, W.; David, C.; Davidek, T.; Davies, E.; Davies, M.; Davignon, O.; Davison, A. R.; Davison, P.; Davygora, Y.; Dawe, E.; Dawson, I.; Daya-Ishmukhametova, R. K.; de, K.; de Asmundis, R.; de Castro, S.; de Cecco, S.; de Graat, J.; de Groot, N.; de Jong, P.; de La Taille, C.; de la Torre, H.; de Lorenzi, F.; de Nooij, L.; de Pedis, D.; de Salvo, A.; de Sanctis, U.; de Santo, A.; de Vivie de Regie, J. B.; de Zorzi, G.; Dearnaley, W. J.; Debbe, R.; Debenedetti, C.; Dechenaux, B.; Dedovich, D. V.; Degenhardt, J.; Deigaard, I.; Del Peso, J.; Del Prete, T.; Deliot, F.; Delitzsch, C. M.; Deliyergiyev, M.; Dell'Acqua, A.; Dell'Asta, L.; Dell'Orso, M.; Della Pietra, M.; Della Volpe, D.; Delmastro, M.; Delsart, P. A.; Deluca, C.; Demers, S.; Demichev, M.; Demilly, A.; Denisov, S. P.; Derendarz, D.; Derkaoui, J. E.; Derue, F.; Dervan, P.; Desch, K.; Deterre, C.; Deviveiros, P. O.; Dewhurst, A.; Dhaliwal, S.; di Ciaccio, A.; di Ciaccio, L.; di Domenico, A.; di Donato, C.; di Girolamo, A.; di Girolamo, B.; di Mattia, A.; di Micco, B.; di Nardo, R.; di Simone, A.; di Sipio, R.; di Valentino, D.; Diaz, M. A.; Diehl, E. B.; Dietrich, J.; Dietzsch, T. A.; Diglio, S.; Dimitrievska, A.; Dingfelder, J.; Dionisi, C.; Dita, P.; Dita, S.; Dittus, F.; Djama, F.; Djobava, T.; Do Vale, M. A. B.; Do Valle Wemans, A.; Doan, T. K. O.; Dobos, D.; Dobson, E.; Doglioni, C.; Doherty, T.; Dohmae, T.; Dolejsi, J.; Dolezal, Z.; Dolgoshein, B. A.; Donadelli, M.; Donati, S.; Dondero, P.; Donini, J.; Dopke, J.; Doria, A.; Dos Anjos, A.; Dova, M. T.; Doyle, A. T.; Dris, M.; Dubbert, J.; Dube, S.; Dubreuil, E.; Duchovni, E.; Duckeck, G.; Ducu, O. A.; Duda, D.; Dudarev, A.; Dudziak, F.; Duflot, L.; Duguid, L.; Dührssen, M.; Dunford, M.; Duran Yildiz, H.; Düren, M.; Durglishvili, A.; Dwuznik, M.; Dyndal, M.; Ebke, J.; Edson, W.; Edwards, N. C.; Ehrenfeld, W.; Eifert, T.; Eigen, G.; Einsweiler, K.; Ekelof, T.; El Kacimi, M.; Ellert, M.; Elles, S.; Ellinghaus, F.; Ellis, N.; Elmsheuser, J.; Elsing, M.; Emeliyanov, D.; Enari, Y.; Endner, O. C.; Endo, M.; Engelmann, R.; Erdmann, J.; Ereditato, A.; Eriksson, D.; Ernis, G.; Ernst, J.; Ernst, M.; Ernwein, J.; Errede, D.; Errede, S.; Ertel, E.; Escalier, M.; Esch, H.; Escobar, C.; Esposito, B.; Etienvre, A. I.; Etzion, E.; Evans, H.; Fabbri, L.; Facini, G.; Fakhrutdinov, R. M.; Falciano, S.; Fang, Y.; Fanti, M.; Farbin, A.; Farilla, A.; Farooque, T.; Farrell, S.; Farrington, S. M.; Farthouat, P.; Fassi, F.; Fassnacht, P.; Fassouliotis, D.; Favareto, A.; Fayard, L.; Federic, P.; Fedin, O. L.; Fedorko, W.; Fehling-Kaschek, M.; Feigl, S.; Feligioni, L.; Feng, C.; Feng, E. J.; Feng, H.; Fenyuk, A. B.; Fernandez Perez, S.; Ferrag, S.; Ferrando, J.; Ferrara, V.; Ferrari, A.; Ferrari, P.; Ferrari, R.; Ferreira de Lima, D. E.; Ferrer, A.; Ferrere, D.; Ferretti, C.; Ferretto Parodi, A.; Fiascaris, M.; Fiedler, F.; Filipčič, A.; Filipuzzi, M.; Filthaut, F.; Fincke-Keeler, M.; Finelli, K. D.; Fiolhais, M. C. N.; Fiorini, L.; Firan, A.; Fischer, J.; Fisher, M. J.; Fisher, W. C.; Fitzgerald, E. A.; Flechl, M.; Fleck, I.; Fleischmann, P.; Fleischmann, S.; Fletcher, G. T.; Fletcher, G.; Flick, T.; Floderus, A.; Flores Castillo, L. R.; Florez Bustos, A. C.; Flowerdew, M. J.; Formica, A.; Forti, A.; Fortin, D.; Fournier, D.; Fox, H.; Fracchia, S.; Francavilla, P.; Franchini, M.; Franchino, S.; Francis, D.; Franklin, M.; Franz, S.; Fraternali, M.; French, S. T.; Friedrich, C.; Friedrich, F.; Froidevaux, D.; Frost, J. A.; Fukunaga, C.; Fullana Torregrosa, E.; Fulsom, B. G.; Fuster, J.; Gabaldon, C.; Gabizon, O.; Gabrielli, A.; Gabrielli, A.; Gadatsch, S.; Gadomski, S.; Gagliardi, G.; Gagnon, P.; Galea, C.; Galhardo, B.; Gallas, E. J.; Gallo, V.; Gallop, B. J.; Gallus, P.; Galster, G.; Gan, K. K.; Gandrajula, R. P.; Gao, J.; Gao, Y. S.; Garay Walls, F. M.; Garberson, F.; García, C.; García Navarro, J. E.; Garcia-Sciveres, M.; Gardner, R. W.; Garelli, N.; Garonne, V.; Gatti, C.; Gaudio, G.; Gaur, B.; Gauthier, L.; Gauzzi, P.; Gavrilenko, I. L.; Gay, C.; Gaycken, G.; Gazis, E. N.; Ge, P.; Gecse, Z.; Gee, C. N. P.; Geerts, D. A. A.; Geich-Gimbel, Ch.; Gellerstedt, K.; Gemme, C.; Gemmell, A.; Genest, M. H.; Gentile, S.; George, M.; George, S.; Gerbaudo, D.; Gershon, A.; Ghazlane, H.; Ghodbane, N.; Giacobbe, B.; Giagu, S.; Giangiobbe, V.; Giannetti, P.; Gianotti, F.; Gibbard, B.; Gibson, S. M.; Gilchriese, M.; Gillam, T. P. S.; Gillberg, D.; Gilles, G.; Gingrich, D. M.; Giokaris, N.; Giordani, M. P.; Giordano, R.; Giorgi, F. M.; Giraud, P. F.; Giugni, D.; Giuliani, C.; Giulini, M.; Gjelsten, B. K.; Gkialas, I.; Gladilin, L. K.; Glasman, C.; Glatzer, J.; Glaysher, P. C. F.; Glazov, A.; Glonti, G. L.; Goblirsch-Kolb, M.; Goddard, J. R.; Godfrey, J.; Godlewski, J.; Goeringer, C.; Goldfarb, S.; Golling, T.; Golubkov, D.; Gomes, A.; Gomez Fajardo, L. S.; Gonçalo, R.; Goncalves Pinto Firmino da Costa, J.; Gonella, L.; González de La Hoz, S.; Gonzalez Parra, G.; Gonzalez Silva, M. L.; Gonzalez-Sevilla, S.; Goossens, L.; Gorbounov, P. A.; Gordon, H. A.; Gorelov, I.; Gorfine, G.; Gorini, B.; Gorini, E.; Gorišek, A.; Gornicki, E.; Goshaw, A. T.; Gössling, C.; Gostkin, M. I.; Gouighri, M.; Goujdami, D.; Goulette, M. P.; Goussiou, A. G.; Goy, C.; Gozpinar, S.; Grabas, H. M. X.; Graber, L.; Grabowska-Bold, I.; Grafström, P.; Grahn, K.-J.; Gramling, J.; Gramstad, E.; Grancagnolo, F.; Grancagnolo, S.; Grassi, V.; Gratchev, V.; Gray, H. M.; Graziani, E.; Grebenyuk, O. G.; Greenwood, Z. D.; Gregersen, K.; Gregor, I. M.; Grenier, P.; Griffiths, J.; Grigalashvili, N.; Grillo, A. A.; Grimm, K.; Grinstein, S.; Gris, Ph.; Grishkevich, Y. V.; Grivaz, J.-F.; Grohs, J. P.; Grohsjean, A.; Gross, E.; Grosse-Knetter, J.; Grossi, G. C.; Groth-Jensen, J.; Grout, Z. J.; Grybel, K.; Guan, L.; Guescini, F.; Guest, D.; Gueta, O.; Guicheney, C.; Guido, E.; Guillemin, T.; Guindon, S.; Gul, U.; Gumpert, C.; Gunther, J.; Guo, J.; Gupta, S.; Gutierrez, P.; Gutierrez Ortiz, N. G.; Gutschow, C.; Guttman, N.; Guyot, C.; Gwenlan, C.; Gwilliam, C. B.; Haas, A.; Haber, C.; Hadavand, H. K.; Haddad, N.; Haefner, P.; Hageboeck, S.; Hajduk, Z.; Hakobyan, H.; Haleem, M.; Hall, D.; Halladjian, G.; Hamacher, K.; Hamal, P.; Hamano, K.; Hamer, M.; Hamilton, A.; Hamilton, S.; Hamnett, P. G.; Han, L.; Hanagaki, K.; Hanawa, K.; Hance, M.; Hanke, P.; Hansen, J. R.; Hansen, J. B.; Hansen, J. D.; Hansen, P. H.; Hara, K.; Hard, A. S.; Harenberg, T.; Harkusha, S.; Harper, D.; Harrington, R. D.; Harris, O. M.; Harrison, P. F.; Hartjes, F.; Hasegawa, S.; Hasegawa, Y.; Hasib, A.; Hassani, S.; Haug, S.; Hauschild, M.; Hauser, R.; Havranek, M.; Hawkes, C. M.; Hawkings, R. J.; Hawkins, A. D.; Hayashi, T.; Hayden, D.; Hays, C. P.; Hayward, H. S.; Haywood, S. J.; Head, S. J.; Heck, T.; Hedberg, V.; Heelan, L.; Heim, S.; Heim, T.; Heinemann, B.; Heinrich, L.; Heisterkamp, S.; Hejbal, J.; Helary, L.; Heller, C.; Heller, M.; Hellman, S.; Hellmich, D.; Helsens, C.; Henderson, J.; Henderson, R. C. W.; Hengler, C.; Henrichs, A.; Henriques Correia, A. M.; Henrot-Versille, S.; Hensel, C.; Herbert, G. H.; Hernández Jiménez, Y.; Herrberg-Schubert, R.; Herten, G.; Hertenberger, R.; Hervas, L.; Hesketh, G. G.; Hessey, N. P.; Hickling, R.; Higón-Rodriguez, E.; Hill, J. C.; Hiller, K. H.; Hillert, S.; Hillier, S. J.; Hinchliffe, I.; Hines, E.; Hirose, M.; Hirschbuehl, D.; Hobbs, J.; Hod, N.; Hodgkinson, M. C.; Hodgson, P.; Hoecker, A.; Hoeferkamp, M. R.; Hoffman, J.; Hoffmann, D.; Hofmann, J. I.; Hohlfeld, M.; Holmes, T. R.; Hong, T. M.; Hooft van Huysduynen, L.; Hostachy, J.-Y.; Hou, S.; Hoummada, A.; Howard, J.; Howarth, J.; Hrabovsky, M.; Hristova, I.; Hrivnac, J.; Hryn'ova, T.; Hsu, P. J.; Hsu, S.-C.; Hu, D.; Hu, X.; Huang, Y.; Hubacek, Z.; Hubaut, F.; Huegging, F.; Huffman, T. B.; Hughes, E. W.; Hughes, G.; Huhtinen, M.; Hülsing, T. A.; Hurwitz, M.; Huseynov, N.; Huston, J.; Huth, J.; Iacobucci, G.; Iakovidis, G.; Ibragimov, I.; Iconomidou-Fayard, L.; Idarraga, J.; Ideal, E.; Iengo, P.; Igonkina, O.; Iizawa, T.; Ikegami, Y.; Ikematsu, K.; Ikeno, M.; Iliadis, D.; Ilic, N.; Inamaru, Y.; Ince, T.; Ioannou, P.; Iodice, M.; Iordanidou, K.; Ippolito, V.; Irles Quiles, A.; Isaksson, C.; Ishino, M.; Ishitsuka, M.; Ishmukhametov, R.; Issever, C.; Istin, S.; Iturbe Ponce, J. M.; Ivashin, A. V.; Iwanski, W.; Iwasaki, H.; Izen, J. M.; Izzo, V.; Jackson, B.; Jackson, J. N.; Jackson, M.; Jackson, P.; Jaekel, M. R.; Jain, V.; Jakobs, K.; Jakobsen, S.; Jakoubek, T.; Jakubek, J.; Jamin, D. O.; Jana, D. K.; Jansen, E.; Jansen, H.; Janssen, J.; Janus, M.; Jarlskog, G.; Javå¯Rek, T.; Jeanty, L.; Jeng, G.-Y.; Jennens, D.; Jenni, P.; Jentzsch, J.; Jeske, C.; Jézéquel, S.; Ji, H.; Ji, W.; Jia, J.; Jiang, Y.; Jimenez Belenguer, M.; Jin, S.; Jinaru, A.; Jinnouchi, O.; Joergensen, M. D.; Johansson, K. E.; Johansson, P.; Johns, K. A.; Jon-And, K.; Jones, G.; Jones, R. W. L.; Jones, T. J.; Jongmanns, J.; Jorge, P. M.; Joshi, K. D.; Jovicevic, J.; Ju, X.; Jung, C. A.; Jungst, R. M.; Jussel, P.; Juste Rozas, A.; Kaci, M.; Kaczmarska, A.; Kado, M.; Kagan, H.; Kagan, M.; Kajomovitz, E.; Kama, S.; Kanaya, N.; Kaneda, M.; Kaneti, S.; Kanno, T.; Kantserov, V. A.; Kanzaki, J.; Kaplan, B.; Kapliy, A.; Kar, D.; Karakostas, K.; Karastathis, N.; Karnevskiy, M.; Karpov, S. N.; Karthik, K.; Kartvelishvili, V.; Karyukhin, A. N.; Kashif, L.; Kasieczka, G.; Kass, R. D.; Kastanas, A.; Kataoka, Y.; Katre, A.; Katzy, J.; Kaushik, V.; Kawagoe, K.; Kawamoto, T.; Kawamura, G.; Kazama, S.; Kazanin, V. F.; Kazarinov, M. Y.; Keeler, R.; Keener, P. T.; Kehoe, R.; Keil, M.; Keller, J. S.; Keoshkerian, H.; Kepka, O.; Kerševan, B. P.; Kersten, S.; Kessoku, K.; Keung, J.; Khalil-Zada, F.; Khandanyan, H.; Khanov, A.; Khodinov, A.; Khomich, A.; Khoo, T. J.; Khoriauli, G.; Khoroshilov, A.; Khovanskiy, V.; Khramov, E.; Khubua, J.; Kim, H. Y.; Kim, H.; Kim, S. H.; Kimura, N.; Kind, O.; King, B. T.; King, M.; King, R. S. B.; King, S. B.; Kirk, J.; Kiryunin, A. E.; Kishimoto, T.; Kisielewska, D.; Kiss, F.; Kitamura, T.; Kittelmann, T.; Kiuchi, K.; Kladiva, E.; Klein, M.; Klein, U.; Kleinknecht, K.; Klimek, P.; Klimentov, A.; Klingenberg, R.; Klinger, J. A.; Klinkby, E. B.; Klioutchnikova, T.; Klok, P. F.; Kluge, E.-E.; Kluit, P.; Kluth, S.; Kneringer, E.; Knoops, E. B. F. G.; Knue, A.; Kobayashi, T.; Kobel, M.; Kocian, M.; Kodys, P.; Koevesarki, P.; Koffas, T.; Koffeman, E.; Kogan, L. A.; Kohlmann, S.; Kohout, Z.; Kohriki, T.; Koi, T.; Kolanoski, H.; Koletsou, I.; Koll, J.; Komar, A. A.; Komori, Y.; Kondo, T.; Kondrashova, N.; Köneke, K.; König, A. C.; König, S.; Kono, T.; Konoplich, R.; Konstantinidis, N.; Kopeliansky, R.; Koperny, S.; Köpke, L.; Kopp, A. K.; Korcyl, K.; Kordas, K.; Korn, A.; Korol, A. A.; Korolkov, I.; Korolkova, E. V.; Korotkov, V. A.; Kortner, O.; Kortner, S.; Kostyukhin, V. V.; Kotov, S.; Kotov, V. M.; Kotwal, A.; Kourkoumelis, C.; Kouskoura, V.; Koutsman, A.; Kowalewski, R.; Kowalski, T. Z.; Kozanecki, W.; Kozhin, A. S.; Kral, V.; Kramarenko, V. A.; Kramberger, G.; Krasnopevtsev, D.; Krasny, M. W.; Krasznahorkay, A.; Kraus, J. K.; Kravchenko, A.; Kreiss, S.; Kretz, M.; Kretzschmar, J.; Kreutzfeldt, K.; Krieger, P.; Kroeninger, K.; Kroha, H.; Kroll, J.; Kroseberg, J.; Krstic, J.; Kruchonak, U.; Krüger, H.; Kruker, T.; Krumnack, N.; Krumshteyn, Z. V.; Kruse, A.; Kruse, M. C.; Kruskal, M.; Kubota, T.; Kuday, S.; Kuehn, S.; Kugel, A.; Kuhl, A.; Kuhl, T.; Kukhtin, V.; Kulchitsky, Y.; Kuleshov, S.; Kuna, M.; Kunkle, J.; Kupco, A.; Kurashige, H.; Kurochkin, Y. A.; Kurumida, R.; Kus, V.; Kuwertz, E. S.; Kuze, M.; Kvita, J.; La Rosa, A.; La Rotonda, L.; Labarga, L.; Lacasta, C.; Lacava, F.; Lacey, J.; Lacker, H.; Lacour, D.; Lacuesta, V. R.; Ladygin, E.; Lafaye, R.; Laforge, B.; Lagouri, T.; Lai, S.; Laier, H.; Lambourne, L.; Lammers, S.; Lampen, C. L.; Lampl, W.; Lançon, E.; Landgraf, U.; Landon, M. P. J.; Lang, V. S.; Lange, C.; Lankford, A. J.; Lanni, F.; Lantzsch, K.; Lanza, A.; Laplace, S.; Lapoire, C.; Laporte, J. F.; Lari, T.; Lassnig, M.; Laurelli, P.; Lavorini, V.; Lavrijsen, W.; Law, A. T.; Laycock, P.; Le, B. T.; Le Dortz, O.; Le Guirriec, E.; Le Menedeu, E.; Lecompte, T.; Ledroit-Guillon, F.; Lee, C. A.; Lee, H.; Lee, J. S. H.; Lee, S. C.; Lee, L.; Lefebvre, G.; Lefebvre, M.; Legger, F.; Leggett, C.; Lehan, A.; Lehmacher, M.; Lehmann Miotto, G.; Lei, X.; Leister, A. G.; Leite, M. A. L.; Leitner, R.; Lellouch, D.; Lemmer, B.; Leney, K. J. C.; Lenz, T.; Lenzen, G.; Lenzi, B.; Leone, R.; Leonhardt, K.; Leontsinis, S.; Leroy, C.; Lester, C. G.; Lester, C. M.; Levêque, J.; Levin, D.; Levinson, L. J.; Levy, M.; Lewis, A.; Lewis, G. H.; Leyko, A. M.; Leyton, M.; Li, B.; Li, B.; Li, H.; Li, H. L.; Li, S.; Li, X.; Li, Y.; Liang, Z.; Liao, H.; Liberti, B.; Lichard, P.; Lie, K.; Liebal, J.; Liebig, W.; Limbach, C.; Limosani, A.; Limper, M.; Lin, S. C.; Linde, F.; Lindquist, B. E.; Linnemann, J. T.; Lipeles, E.; Lipniacka, A.; Lisovyi, M.; Liss, T. M.; Lissauer, D.; Lister, A.; Litke, A. M.; Liu, B.; Liu, D.; Liu, J. B.; Liu, K.; Liu, L.; Liu, M.; Liu, M.; Liu, Y.; Livan, M.; Livermore, S. S. A.; Lleres, A.; Llorente Merino, J.; Lloyd, S. L.; Lo Sterzo, F.; Lobodzinska, E.; Loch, P.; Lockman, W. S.; Loddenkoetter, T.; Loebinger, F. K.; Loevschall-Jensen, A. E.; Loginov, A.; Loh, C. W.; Lohse, T.; Lohwasser, K.; Lokajicek, M.; Lombardo, V. P.; Long, J. D.; Long, R. E.; Lopes, L.; Lopez Mateos, D.; Lopez Paredes, B.; Lorenz, J.; Lorenzo Martinez, N.; Losada, M.; Loscutoff, P.; Lou, X.; Lounis, A.; Love, J.; Love, P. A.; Lowe, A. J.; Lu, F.; Lubatti, H. J.; Luci, C.; Lucotte, A.; Luehring, F.; Lukas, W.; Luminari, L.; Lundberg, O.; Lund-Jensen, B.; Lungwitz, M.; Lynn, D.; Lysak, R.; Lytken, E.; Ma, H.; Ma, L. L.; Maccarrone, G.; Macchiolo, A.; Maček, B.; Machado Miguens, J.; Macina, D.; Madaffari, D.; Madar, R.; Maddocks, H. J.; Mader, W. F.; Madsen, A.; Maeno, M.; Maeno, T.; Magradze, E.; Mahboubi, K.; Mahlstedt, J.; Mahmoud, S.; Maiani, C.; Maidantchik, C.; Maio, A.; Majewski, S.; Makida, Y.; Makovec, N.; Mal, P.; Malaescu, B.; Malecki, Pa.; Maleev, V. P.; Malek, F.; Mallik, U.; Malon, D.; Malone, C.; Maltezos, S.; Malyshev, V. M.; Malyukov, S.; Mamuzic, J.; Mandelli, B.; Mandelli, L.; Mandić, I.; Mandrysch, R.; Maneira, J.; Manfredini, A.; Manhaes de Andrade Filho, L.; Manjarres Ramos, J. A.; Mann, A.; Manning, P. M.; Manousakis-Katsikakis, A.; Mansoulie, B.; Mantifel, R.; Mapelli, L.; March, L.; Marchand, J. F.; Marchiori, G.; Marcisovsky, M.; Marino, C. P.; Marques, C. N.; Marroquim, F.; Marsden, S. P.; Marshall, Z.; Marti, L. F.; Marti-Garcia, S.; Martin, B.; Martin, B.; Martin, J. P.; Martin, T. A.; Martin, V. J.; Martin Dit Latour, B.; Martinez, H.; Martinez, M.; Martin-Haugh, S.; Martyniuk, A. C.; Marx, M.; Marzano, F.; Marzin, A.; Masetti, L.; Mashimo, T.; Mashinistov, R.; Masik, J.; Maslennikov, A. L.; Massa, I.; Massol, N.; Mastrandrea, P.; Mastroberardino, A.; Masubuchi, T.; Matricon, P.; Matsunaga, H.; Matsushita, T.; Mättig, P.; Mättig, S.; Mattmann, J.; Maurer, J.; Maxfield, S. J.; Maximov, D. A.; Mazini, R.; Mazzaferro, L.; Mc Goldrick, G.; Mc Kee, S. P.; McCarn, A.; McCarthy, R. L.; McCarthy, T. G.; McCubbin, N. A.; McFarlane, K. W.; McFayden, J. A.; McHedlidze, G.; McLaughlan, T.; McMahon, S. J.; McPherson, R. A.; Meade, A.; Mechnich, J.; Medinnis, M.; Meehan, S.; Meera-Lebbai, R.; Mehlhase, S.; Mehta, A.; Meier, K.; Meineck, C.; Meirose, B.; Melachrinos, C.; Mellado Garcia, B. R.; Meloni, F.; Mengarelli, A.; Menke, S.; Meoni, E.; Mercurio, K. M.; Mergelmeyer, S.; Meric, N.; Mermod, P.; Merola, L.; Meroni, C.; Merritt, F. S.; Merritt, H.; Messina, A.; Metcalfe, J.; Mete, A. S.; Meyer, C.; Meyer, C.; Meyer, J.-P.; Meyer, J.; Middleton, R. P.; Migas, S.; Mijović, L.; Mikenberg, G.; Mikestikova, M.; Mikuž, M.; Miller, D. W.; Mills, C.; Milov, A.; Milstead, D. A.; Milstein, D.; Minaenko, A. A.; Miñano Moya, M.; Minashvili, I. A.; Mincer, A. I.; Mindur, B.; Mineev, M.; Ming, Y.; Mir, L. M.; Mirabelli, G.; Mitani, T.; Mitrevski, J.; Mitsou, V. A.; Mitsui, S.; Miucci, A.; Miyagawa, P. S.; Mjörnmark, J. U.; Moa, T.; Mochizuki, K.; Moeller, V.; Mohapatra, S.; Mohr, W.; Molander, S.; Moles-Valls, R.; Mönig, K.; Monini, C.; Monk, J.; Monnier, E.; Montejo Berlingen, J.; Monticelli, F.; Monzani, S.; Moore, R. W.; Mora Herrera, C.; Moraes, A.; Morange, N.; Morel, J.; Moreno, D.; Moreno Llácer, M.; Morettini, P.; Morgenstern, M.; Morii, M.; Moritz, S.; Morley, A. K.; Mornacchi, G.; Morris, J. D.; Morvaj, L.; Moser, H. G.; Mosidze, M.; Moss, J.; Mount, R.; Mountricha, E.; Mouraviev, S. V.; Moyse, E. J. W.; Muanza, S.; Mudd, R. D.; Mueller, F.; Mueller, J.; Mueller, K.; Mueller, T.; Mueller, T.; Muenstermann, D.; Munwes, Y.; Murillo Quijada, J. A.; Murray, W. J.; Musheghyan, H.; Musto, E.; Myagkov, A. G.; Myska, M.; Nackenhorst, O.; Nadal, J.; Nagai, K.; Nagai, R.; Nagai, Y.; Nagano, K.; Nagarkar, A.; Nagasaka, Y.; Nagel, M.; Nairz, A. M.; Nakahama, Y.; Nakamura, K.; Nakamura, T.; Nakano, I.; Namasivayam, H.; Nanava, G.; Narayan, R.; Nattermann, T.; Naumann, T.; Navarro, G.; Nayyar, R.; Neal, H. A.; Nechaeva, P. Yu.; Neep, T. J.; Negri, A.; Negri, G.; Negrini, M.; Nektarijevic, S.; Nelson, A.; Nelson, T. K.; Nemecek, S.; Nemethy, P.; Nepomuceno, A. A.; Nessi, M.; Neubauer, M. S.; Neumann, M.; Neves, R. M.; Nevski, P.; Newcomer, F. M.; Newman, P. R.; Nguyen, D. H.; Nickerson, R. B.; Nicolaidou, R.; Nicquevert, B.; Nielsen, J.; Nikiforou, N.; Nikiforov, A.; Nikolaenko, V.; Nikolic-Audit, I.; Nikolics, K.; Nikolopoulos, K.; Nilsson, P.; Ninomiya, Y.; Nisati, A.; Nisius, R.; Nobe, T.; Nodulman, L.; Nomachi, M.; Nomidis, I.; Norberg, S.; Nordberg, M.; Novakova, J.; Nowak, S.; Nozaki, M.; Nozka, L.; Ntekas, K.; Nunes Hanninger, G.; Nunnemann, T.; Nurse, E.; Nuti, F.; O'Brien, B. J.; O'Grady, F.; O'Neil, D. C.; O'Shea, V.; Oakham, F. G.; Oberlack, H.; Obermann, T.; Ocariz, J.; Ochi, A.; Ochoa, M. I.; Oda, S.; Odaka, S.; Ogren, H.; Oh, A.; Oh, S. H.; Ohm, C. C.; Ohman, H.; Ohshima, T.; Okamura, W.; Okawa, H.; Okumura, Y.; Okuyama, T.; Olariu, A.; Olchevski, A. G.; Olivares Pino, S. A.; Oliveira Damazio, D.; Oliver Garcia, E.; Olivito, D.; Olszewski, A.; Olszowska, J.; Onofre, A.; Onyisi, P. U. E.; Oram, C. J.; Oreglia, M. J.; Oren, Y.; Orestano, D.; Orlando, N.; Oropeza Barrera, C.; Orr, R. S.; Osculati, B.; Ospanov, R.; Otero Y Garzon, G.; Otono, H.; Ouchrif, M.; Ouellette, E. A.; Ould-Saada, F.; Ouraou, A.; Oussoren, K. P.; Ouyang, Q.; Ovcharova, A.; Owen, M.; Ozcan, V. E.; Ozturk, N.; Pachal, K.; Pacheco Pages, A.; Padilla Aranda, C.; Pagáčová, M.; Pagan Griso, S.; Paganis, E.; Pahl, C.; Paige, F.; Pais, P.; Pajchel, K.; Palacino, G.; Palestini, S.; Pallin, D.; Palma, A.; Palmer, J. D.; Pan, Y. B.; Panagiotopoulou, E.; Panduro Vazquez, J. G.; Pani, P.; Panikashvili, N.; Panitkin, S.; Pantea, D.; Paolozzi, L.; Papadopoulou, Th. D.; Papageorgiou, K.; Paramonov, A.; Paredes Hernandez, D.; Parker, M. A.; Parodi, F.; Parsons, J. A.; Parzefall, U.; Pasqualucci, E.; Passaggio, S.; Passeri, A.; Pastore, F.; Pastore, Fr.; Pásztor, G.; Pataraia, S.; Patel, N. D.; Pater, J. R.; Patricelli, S.; Pauly, T.; Pearce, J.; Pedersen, M.; Pedraza Lopez, S.; Pedro, R.; Peleganchuk, S. V.; Pelikan, D.; Peng, H.; Penning, B.; Penwell, J.; Perepelitsa, D. V.; Perez Codina, E.; Pérez García-Estañ, M. T.; Perez Reale, V.; Perini, L.; Pernegger, H.; Perrino, R.; Peschke, R.; Peshekhonov, V. D.; Peters, K.; Peters, R. F. Y.; Petersen, B. A.; Petersen, J.; Petersen, T. C.; Petit, E.; Petridis, A.; Petridou, C.; Petrolo, E.; Petrucci, F.; Petteni, M.; Pettersson, N. E.; Pezoa, R.; Phillips, P. W.; Piacquadio, G.; Pianori, E.; Picazio, A.; Piccaro, E.; Piccinini, M.; Piec, S. M.; Piegaia, R.; Pignotti, D. T.; Pilcher, J. E.; Pilkington, A. D.; Pina, J.; Pinamonti, M.; Pinder, A.; Pinfold, J. L.; Pingel, A.; Pinto, B.; Pires, S.; Pizio, C.; Pleier, M.-A.; Pleskot, V.; Plotnikova, E.; Plucinski, P.; Poddar, S.; Podlyski, F.; Poettgen, R.; Poggioli, L.; Pohl, D.; Pohl, M.; Polesello, G.; Policicchio, A.; Polifka, R.; Polini, A.; Pollard, C. S.; Polychronakos, V.; Pommès, K.; Pontecorvo, L.; Pope, B. G.; Popeneciu, G. A.; Popovic, D. S.; Poppleton, A.; Portell Bueso, X.; Pospelov, G. E.; Pospisil, S.; Potamianos, K.; Potrap, I. N.; Potter, C. J.; Potter, C. T.; Poulard, G.; Poveda, J.; Pozdnyakov, V.; Prabhu, R.; Pralavorio, P.; Pranko, A.; Prasad, S.; Pravahan, R.; Prell, S.; Price, D.; Price, J.; Price, L. E.; Prieur, D.; Primavera, M.; Proissl, M.; Prokofiev, K.; Prokoshin, F.; Protopapadaki, E.; Protopopescu, S.; Proudfoot, J.; Przybycien, M.; Przysiezniak, H.; Ptacek, E.; Pueschel, E.; Puldon, D.; Purohit, M.; Puzo, P.; Pylypchenko, Y.; Qian, J.; Qin, G.; Quadt, A.; Quarrie, D. R.; Quayle, W. B.; Quilty, D.; Qureshi, A.; Radeka, V.; Radescu, V.; Radhakrishnan, S. K.; Radloff, P.; Rados, P.; Ragusa, F.; Rahal, G.; Rajagopalan, S.; Rammensee, M.; Rammes, M.; Randle-Conde, A. S.; Rangel-Smith, C.; Rao, K.; Rauscher, F.; Rave, T. C.; Ravenscroft, T.; Raymond, M.; Read, A. L.; Rebuzzi, D. M.; Redelbach, A.; Redlinger, G.; Reece, R.; Reeves, K.; Rehnisch, L.; Reinsch, A.; Reisin, H.; Relich, M.; Rembser, C.; Ren, Z. L.; Renaud, A.; Rescigno, M.; Resconi, S.; Resende, B.; Reznicek, P.; Rezvani, R.; Richter, R.; Ridel, M.; Rieck, P.; Rijssenbeek, M.; Rimoldi, A.; Rinaldi, L.; Ritsch, E.; Riu, I.; Rizatdinova, F.; Rizvi, E.; Robertson, S. H.; Robichaud-Veronneau, A.; Robinson, D.; Robinson, J. E. M.; Robson, A.; Roda, C.; Rodrigues, L.; Roe, S.; Røhne, O.; Rolli, S.; Romaniouk, A.; Romano, M.; Romeo, G.; Romero Adam, E.; Rompotis, N.; Roos, L.; Ros, E.; Rosati, S.; Rosbach, K.; Rose, M.; Rosendahl, P. L.; Rosenthal, O.; Rossetti, V.; Rossi, E.; Rossi, L. P.; Rosten, R.; Rotaru, M.; Roth, I.; Rothberg, J.; Rousseau, D.; Royon, C. R.; Rozanov, A.; Rozen, Y.; Ruan, X.; Rubbo, F.; Rubinskiy, I.; Rud, V. I.; Rudolph, C.; Rudolph, M. S.; Rühr, F.; Ruiz-Martinez, A.; Rurikova, Z.; Rusakovich, N. A.; Ruschke, A.; Rutherfoord, J. P.; Ruthmann, N.; Ryabov, Y. F.; Rybar, M.; Rybkin, G.; Ryder, N. C.; Saavedra, A. F.; Sacerdoti, S.; Saddique, A.; Sadeh, I.; Sadrozinski, H. F.-W.; Sadykov, R.; Safai Tehrani, F.; Sakamoto, H.; Sakurai, Y.; Salamanna, G.; Salamon, A.; Saleem, M.; Salek, D.; Sales de Bruin, P. H.; Salihagic, D.; Salnikov, A.; Salt, J.; Salvachua Ferrando, B. M.; Salvatore, D.; Salvatore, F.; Salvucci, A.; Salzburger, A.; Sampsonidis, D.; Sanchez, A.; Sánchez, J.; Sanchez Martinez, V.; Sandaker, H.; Sander, H. G.; Sanders, M. P.; Sandhoff, M.; Sandoval, T.; Sandoval, C.; Sandstroem, R.; Sankey, D. P. C.; Sansoni, A.; Santoni, C.; Santonico, R.; Santos, H.; Santoyo Castillo, I.; Sapp, K.; Sapronov, A.; Saraiva, J. G.; Sarrazin, B.; Sartisohn, G.; Sasaki, O.; Sasaki, Y.; Satsounkevitch, I.; Sauvage, G.; Sauvan, E.; Savard, P.; Savu, D. O.; Sawyer, C.; Sawyer, L.; Saxon, D. H.; Saxon, J.; Sbarra, C.; Sbrizzi, A.; Scanlon, T.; Scannicchio, D. A.; Scarcella, M.; Schaarschmidt, J.; Schacht, P.; Schaefer, D.; Schaefer, R.; Schaelicke, A.; Schaepe, S.; Schaetzel, S.; Schäfer, U.; Schaffer, A. C.; Schaile, D.; Schamberger, R. D.; Scharf, V.; Schegelsky, V. A.; Scheirich, D.; Schernau, M.; Scherzer, M. I.; Schiavi, C.; Schieck, J.; Schillo, C.; Schioppa, M.; Schlenker, S.; Schmidt, E.; Schmieden, K.; Schmitt, C.; Schmitt, C.; Schmitt, S.; Schneider, B.; Schnellbach, Y. J.; Schnoor, U.; Schoeffel, L.; Schoening, A.; Schoenrock, B. D.; Schorlemmer, A. L. S.; Schott, M.; Schouten, D.; Schovancova, J.; Schram, M.; Schramm, S.; Schreyer, M.; Schroeder, C.; Schuh, N.; Schultens, M. J.; Schultz-Coulon, H.-C.; Schulz, H.; Schumacher, M.; Schumm, B. A.; Schune, Ph.; Schwartzman, A.; Schwegler, Ph.; Schwemling, Ph.; Schwienhorst, R.; Schwindling, J.; Schwindt, T.; Schwoerer, M.; Sciacca, F. G.; Scifo, E.; Sciolla, G.; Scott, W. G.; Scuri, F.; Scutti, F.; Searcy, J.; Sedov, G.; Sedykh, E.; Seidel, S. C.; Seiden, A.; Seifert, F.; Seixas, J. M.; Sekhniaidze, G.; Sekula, S. J.; Selbach, K. E.; Seliverstov, D. M.; Sellers, G.; Semprini-Cesari, N.; Serfon, C.; Serin, L.; Serkin, L.; Serre, T.; Seuster, R.; Severini, H.; Sforza, F.; Sfyrla, A.; Shabalina, E.; Shamim, M.; Shan, L. Y.; Shank, J. T.; Shao, Q. T.; Shapiro, M.; Shatalov, P. B.; Shaw, K.; Sherwood, P.; Shimizu, S.; Shimmin, C. O.; Shimojima, M.; Shin, T.; Shiyakova, M.; Shmeleva, A.; Shochet, M. J.; Short, D.; Shrestha, S.; Shulga, E.; Shupe, M. A.; Shushkevich, S.; Sicho, P.; Sidorov, D.; Sidoti, A.; Siegert, F.; Sijacki, Dj.; Silbert, O.; Silva, J.; Silver, Y.; Silverstein, D.; Silverstein, S. B.; Simak, V.; Simard, O.; Simic, Lj.; Simion, S.; Simioni, E.; Simmons, B.; Simoniello, R.; Simonyan, M.; Sinervo, P.; Sinev, N. B.; Sipica, V.; Siragusa, G.; Sircar, A.; Sisakyan, A. N.; Sivoklokov, S. Yu.; Sjölin, J.; Sjursen, T. B.; Skinnari, L. A.; Skottowe, H. P.; Skovpen, K. Yu.; Skubic, P.; Slater, M.; Slavicek, T.; Sliwa, K.; Smakhtin, V.; Smart, B. H.; Smestad, L.; Smirnov, S. Yu.; Smirnov, Y.; Smirnova, L. N.; Smirnova, O.; Smith, K. M.; Smizanska, M.; Smolek, K.; Snesarev, A. A.; Snidero, G.; Snow, J.; Snyder, S.; Sobie, R.; Socher, F.; Sodomka, J.; Soffer, A.; Soh, D. A.; Solans, C. A.; Solar, M.; Solc, J.; Soldatov, E. Yu.; Soldevila, U.; Solfaroli Camillocci, E.; Solodkov, A. A.; Solovyanov, O. V.; Solovyev, V.; Sommer, P.; Song, H. Y.; Soni, N.; Sood, A.; Sopko, V.; Sopko, B.; Sorin, V.; Sosebee, M.; Soualah, R.; Soueid, P.; Soukharev, A. M.; South, D.; Spagnolo, S.; Spanò, F.; Spearman, W. R.; Spighi, R.; Spigo, G.; Spousta, M.; Spreitzer, T.; Spurlock, B.; St. Denis, R. D.; Staerz, S.; Stahlman, J.; Stamen, R.; Stanecka, E.; Stanek, R. W.; Stanescu, C.; Stanescu-Bellu, M.; Stanitzki, M. M.; Stapnes, S.; Starchenko, E. A.; Stark, J.; Staroba, P.; Starovoitov, P.; Staszewski, R.; Stavina, P.; Steele, G.; Steinberg, P.; Stekl, I.; Stelzer, B.; Stelzer, H. J.; Stelzer-Chilton, O.; Stenzel, H.; Stern, S.; Stewart, G. A.; Stillings, J. A.; Stockton, M. C.; Stoebe, M.; Stoerig, K.; Stoicea, G.; Stolte, P.; Stonjek, S.; Stradling, A. R.; Straessner, A.; Strandberg, J.; Strandberg, S.; Strandlie, A.; Strauss, E.; Strauss, M.; Strizenec, P.; Ströhmer, R.; Strom, D. M.; Stroynowski, R.; Stucci, S. A.; Stugu, B.; Styles, N. A.; Su, D.; Su, J.; Subramania, Hs.; Subramaniam, R.; Succurro, A.; Sugaya, Y.; Suhr, C.; Suk, M.; Sulin, V. V.; Sultansoy, S.; Sumida, T.; Sun, X.; Sundermann, J. E.; Suruliz, K.; Susinno, G.; Sutton, M. R.; Suzuki, Y.; Svatos, M.; Swedish, S.; Swiatlowski, M.; Sykora, I.; Sykora, T.; Ta, D.; Tackmann, K.; Taenzer, J.; Taffard, A.; Tafirout, R.; Taiblum, N.; Takahashi, Y.; Takai, H.; Takashima, R.; Takeda, H.; Takeshita, T.; Takubo, Y.; Talby, M.; Talyshev, A. A.; Tam, J. Y. C.; Tamsett, M. C.; Tan, K. G.; Tanaka, J.; Tanaka, R.; Tanaka, S.; Tanaka, S.; Tanasijczuk, A. J.; Tani, K.; Tannoury, N.; Tapprogge, S.; Tarem, S.; Tarrade, F.; Tartarelli, G. F.; Tas, P.; Tasevsky, M.; Tashiro, T.; Tassi, E.; Tavares Delgado, A.; Tayalati, Y.; Taylor, C.; Taylor, F. E.; Taylor, G. N.; Taylor, W.; Teischinger, F. A.; Teixeira Dias Castanheira, M.; Teixeira-Dias, P.; Temming, K. K.; Ten Kate, H.; Teng, P. K.; Terada, S.; Terashi, K.; Terron, J.; Terzo, S.; Testa, M.; Teuscher, R. J.; Therhaag, J.; Theveneaux-Pelzer, T.; Thoma, S.; Thomas, J. P.; Thomas-Wilsker, J.; Thompson, E. N.; Thompson, P. D.; Thompson, P. D.; Thompson, A. S.; Thomsen, L. A.; Thomson, E.; Thomson, M.; Thong, W. M.; Thun, R. P.; Tian, F.; Tibbetts, M. J.; Tikhomirov, V. O.; Tikhonov, Yu. A.; Timoshenko, S.; Tiouchichine, E.; Tipton, P.; Tisserant, S.; Todorov, T.; Todorova-Nova, S.; Toggerson, B.; Tojo, J.; Tokár, S.; Tokushuku, K.; Tollefson, K.; Tomlinson, L.; Tomoto, M.; Tompkins, L.; Toms, K.; Topilin, N. D.; Torrence, E.; Torres, H.; Torró Pastor, E.; Toth, J.; Touchard, F.; Tovey, D. R.; Tran, H. L.; Trefzger, T.; Tremblet, L.; Tricoli, A.; Trigger, I. M.; Trincaz-Duvoid, S.; Tripiana, M. F.; Triplett, N.; Trischuk, W.; Trocmé, B.; Troncon, C.; Trottier-McDonald, M.; Trovatelli, M.; True, P.; Trzebinski, M.; Trzupek, A.; Tsarouchas, C.; Tseng, J. C.-L.; Tsiareshka, P. V.; Tsionou, D.; Tsipolitis, G.; Tsirintanis, N.; Tsiskaridze, S.; Tsiskaridze, V.; Tskhadadze, E. G.; Tsukerman, I. I.; Tsulaia, V.; Tsuno, S.; Tsybychev, D.; Tua, A.; Tudorache, A.; Tudorache, V.; Tuna, A. N.; Tupputi, S. A.; Turchikhin, S.; Turecek, D.; Turk Cakir, I.; Turra, R.; Tuts, P. M.; Tykhonov, A.; Tylmad, M.; Tyndel, M.; Uchida, K.; Ueda, I.; Ueno, R.; Ughetto, M.; Ugland, M.; Uhlenbrock, M.; Ukegawa, F.; Unal, G.; Undrus, A.; Unel, G.; Ungaro, F. C.; Unno, Y.; Urbaniec, D.; Urquijo, P.; Usai, G.; Usanova, A.; Vacavant, L.; Vacek, V.; Vachon, B.; Valencic, N.; Valentinetti, S.; Valero, A.; Valery, L.; Valkar, S.; Valladolid Gallego, E.; Vallecorsa, S.; Valls Ferrer, J. A.; van Berg, R.; van der Deijl, P. C.; van der Geer, R.; van der Graaf, H.; van der Leeuw, R.; van der Ster, D.; van Eldik, N.; van Gemmeren, P.; van Nieuwkoop, J.; van Vulpen, I.; van Woerden, M. C.; Vanadia, M.; Vandelli, W.; Vanguri, R.; Vaniachine, A.; Vankov, P.; Vannucci, F.; Vardanyan, G.; Vari, R.; Varnes, E. W.; Varol, T.; Varouchas, D.; Vartapetian, A.; Varvell, K. E.; Vassilakopoulos, V. I.; Vazeille, F.; Vazquez Schroeder, T.; Veatch, J.; Veloso, F.; Veneziano, S.; Ventura, A.; Ventura, D.; Venturi, M.; Venturi, N.; Venturini, A.; Vercesi, V.; Verducci, M.; Verkerke, W.; Vermeulen, J. C.; Vest, A.; Vetterli, M. C.; Viazlo, O.; Vichou, I.; Vickey, T.; Vickey Boeriu, O. E.; Viehhauser, G. H. A.; Viel, S.; Vigne, R.; Villa, M.; Villaplana Perez, M.; Vilucchi, E.; Vincter, M. G.; Vinogradov, V. B.; Virzi, J.; Vitells, O.; Vivarelli, I.; Vives Vaque, F.; Vlachos, S.; Vladoiu, D.; Vlasak, M.; Vogel, A.; Vokac, P.; Volpi, G.; Volpi, M.; von der Schmitt, H.; von Radziewski, H.; von Toerne, E.; Vorobel, V.; Vorobev, K.; Vos, M.; Voss, R.; Vossebeld, J. H.; Vranjes, N.; Vranjes Milosavljevic, M.; Vrba, V.; Vreeswijk, M.; Vu Anh, T.; Vuillermet, R.; Vukotic, I.; Vykydal, Z.; Wagner, W.; Wagner, P.; Wahrmund, S.; Wakabayashi, J.; Walder, J.; Walker, R.; Walkowiak, W.; Wall, R.; Waller, P.; Walsh, B.; Wang, C.; Wang, C.; Wang, F.; Wang, H.; Wang, H.; Wang, J.; Wang, J.; Wang, K.; Wang, R.; Wang, S. M.; Wang, T.; Wang, X.; Warburton, A.; Ward, C. P.; Wardrope, D. R.; Warsinsky, M.; Washbrook, A.; Wasicki, C.; Watanabe, I.; Watkins, P. M.; Watson, A. T.; Watson, I. J.; Watson, M. F.; Watts, G.; Watts, S.; Waugh, B. M.; Webb, S.; Weber, M. S.; Weber, S. W.; Webster, J. S.; Weidberg, A. R.; Weigell, P.; Weinert, B.; Weingarten, J.; Weiser, C.; Weits, H.; Wells, P. S.; Wenaus, T.; Wendland, D.; Weng, Z.; Wengler, T.; Wenig, S.; Wermes, N.; Werner, M.; Werner, P.; Wessels, M.; Wetter, J.; Whalen, K.; White, A.; White, M. J.; White, R.; White, S.; Whiteson, D.; Wicke, D.; Wickens, F. J.; Wiedenmann, W.; Wielers, M.; Wienemann, P.; Wiglesworth, C.; Wiik-Fuchs, L. A. M.; Wijeratne, P. A.; Wildauer, A.; Wildt, M. A.; Wilkens, H. G.; Will, J. Z.; Williams, H. H.; Williams, S.; Willis, C.; Willocq, S.; Wilson, J. A.; Wilson, A.; Wingerter-Seez, I.; Winkelmann, S.; Winklmeier, F.; Wittgen, M.; Wittig, T.; Wittkowski, J.; Wollstadt, S. J.; Wolter, M. W.; Wolters, H.; Wosiek, B. K.; Wotschack, J.; Woudstra, M. J.; Wozniak, K. W.; Wright, M.; Wu, M.; Wu, S. L.; Wu, X.; Wu, Y.; Wulf, E.; Wyatt, T. R.; Wynne, B. M.; Xella, S.; Xiao, M.; Xu, D.; Xu, L.; Yabsley, B.; Yacoob, S.; Yamada, M.; Yamaguchi, H.; Yamaguchi, Y.; Yamamoto, A.; Yamamoto, K.; Yamamoto, S.; Yamamura, T.; Yamanaka, T.; Yamauchi, K.; Yamazaki, Y.; Yan, Z.; Yang, H.; Yang, H.; Yang, U. K.; Yang, Y.; Yanush, S.; Yao, L.; Yao, W.-M.; Yasu, Y.; Yatsenko, E.; Yau Wong, K. H.; Ye, J.; Ye, S.; Yen, A. L.; Yildirim, E.; Yilmaz, M.; Yoosoofmiya, R.; Yorita, K.; Yoshida, R.; Yoshihara, K.; Young, C.; Young, C. J. S.; Youssef, S.; Yu, D. R.; Yu, J.; Yu, J. M.; Yu, J.; Yuan, L.; Yurkewicz, A.; Zabinski, B.; Zaidan, R.; Zaitsev, A. M.; Zaman, A.; Zambito, S.; Zanello, L.; Zanzi, D.; Zaytsev, A.; Zeitnitz, C.; Zeman, M.; Zemla, A.; Zengel, K.; Zenin, O.; Ženiš, T.; Zerwas, D.; Zevi Della Porta, G.; Zhang, D.; Zhang, F.; Zhang, H.; Zhang, J.; Zhang, L.; Zhang, X.; Zhang, Z.; Zhao, Z.; Zhemchugov, A.; Zhong, J.; Zhou, B.; Zhou, L.; Zhou, N.; Zhu, C. G.; Zhu, H.; Zhu, J.; Zhu, Y.; Zhuang, X.; Zibell, A.; Zieminska, D.; Zimine, N. I.; Zimmermann, C.; Zimmermann, R.; Zimmermann, S.; Zimmermann, S.; Zinonos, Z.; Ziolkowski, M.; Zitoun, R.; Zobernig, G.; Zoccoli, A.; Zur Nedden, M.; Zurzolo, G.; Zutshi, V.; Zwalinski, L.; Atlas Collaboration

2014-05-01

A measurement of the parity-violating decay asymmetry parameter, αb, and the helicity amplitudes for the decay Λb0→J/ψ(μ+μ-)Λ0(pπ-) is reported. The analysis is based on 1400 Λb0 and Λ ¯b0 baryons selected in 4.6 fb-1 of proton-proton collision data with a center-of-mass energy of 7 TeV recorded by the ATLAS experiment at the LHC. By combining the Λb0 and Λ ¯b0 samples under the assumption of CP conservation, the value of αb is measured to be 0.30±0.16(stat)±0.06(syst). This measurement provides a test of theoretical models based on perturbative QCD or heavy-quark effective theory.

The current matrix elements from HAL QCD method

NASA Astrophysics Data System (ADS)

Watanabe, Kai; Ishii, Noriyoshi

2018-03-01

HAL QCD method is a method to construct a potential (HAL QCD potential) that reproduces the NN scattering phase shift faithful to the QCD. The HAL QCD potential is obtained from QCD by eliminating the degrees of freedom of quarks and gluons and leaving only two particular hadrons. Therefor, in the effective quantum mechanics of two nucleons defined by HAL QCD potential, the conserved current consists not only of the nucleon current but also an extra current originating from the potential (two-body current). Though the form of the two-body current is closely related to the potential, it is not straight forward to extract the former from the latter. In this work, we derive the the current matrix element formula in the quantum mechanics defined by the HAL QCD potential. As a first step, we focus on the non-relativistic case. To give an explicit example, we consider a second quantized non-relativistic two-channel coupling model which we refer to as the original model. From the original model, the HAL QCD potential for the open channel is constructed by eliminating the closed channel in the elastic two-particle scattering region. The current matrix element formula is derived by demanding the effective quantum mechanics defined by the HAL QCD potential to respond to the external field in the same way as the original two-channel coupling model.

Selection of a platinum-binding sequence in a loop of a four-helix bundle protein.

PubMed

Yagi, Sota; Akanuma, Satoshi; Kaji, Asumi; Niiro, Hiroya; Akiyama, Hayato; Uchida, Tatsuya; Yamagishi, Akihiko

2018-02-01

Protein-metal hybrids are functional materials with various industrial applications. For example, a redox enzyme immobilized on a platinum electrode is a key component of some biofuel cells and biosensors. To create these hybrid materials, protein molecules are bound to metal surfaces. Here, we report the selection of a novel platinum-binding sequence in a loop of a four-helix bundle protein, the Lac repressor four-helix protein (LARFH), an artificial protein in which four identical α-helices are connected via three identical loops. We created a genetic library in which the Ser-Gly-Gln-Gly-Gly-Ser sequence within the first inter-helical loop of LARFH was semi-randomly mutated. The library was then subjected to selection for platinum-binding affinity by using the T7 phage display method. The majority of the selected variants contained the Tyr-Lys-Arg-Gly-Tyr-Lys (YKRGYK) sequence in their randomized segment. We characterized the platinum-binding properties of mutant LARFH by using quartz crystal microbalance analysis. Mutant LARFH seemed to interact with platinum through its loop containing the YKRGYK sequence, as judged by the estimated exclusive area occupied by a single molecule. Furthermore, a 10-residue peptide containing the YKRGYK sequence bound to platinum with reasonably high affinity and basic side chains in the peptide were crucial in mediating this interaction. In conclusion, we have identified an amino acid sequence, YKRGYK, in the loop of a helix-loop-helix motif that shows high platinum-binding affinity. This sequence could be grafted into loops of other polypeptides as an approach to immobilize proteins on platinum electrodes for use as biosensors among other applications. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Perturbative matching of lattice and continuum heavy-light currents with NRQCD heavy quarks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morningstar, C.J.; Shigemitsu, J.

1999-05-01

The temporal and spatial components of the heavy-light vector current and the spatial components of the axial-vector current are expressed in terms of lattice-regulated operators suitable for simulations of {ital B} and {ital D} mesons. The currents are constructed by matching the appropriate scattering amplitudes in continuum QCD and a lattice model to one-loop order in perturbation theory. In the lattice theory, the heavy quarks are treated using the nonrelativistic (NRQCD) formulation and the light quarks are described by the tadpole-improved clover action. The light quarks are treated as massless. Our currents include relativistic and discretization corrections through O({alpha}{sub s}/M,a{alpha}{submore » s}), where {ital M} is the heavy-quark mass, {ital a} is the lattice spacing, and {alpha}{sub s} is the QCD coupling. As in our previous construction of the temporal component of the heavy-light axial-vector current, mixing between several lattice operators is encountered at one-loop order, and O(a{alpha}{sub s}) dimension-four improvement terms are identified. {copyright} {ital 1999} {ital The American Physical Society}« less

Using infinite-volume, continuum QED and lattice QCD for the hadronic light-by-light contribution to the muon anomalous magnetic moment

NASA Astrophysics Data System (ADS)

Blum, Thomas; Christ, Norman; Hayakawa, Masashi; Izubuchi, Taku; Jin, Luchang; Jung, Chulwoo; Lehner, Christoph

2017-08-01

In our previous work, Blum et al. [Phys. Rev. Lett. 118, 022005 (2017), 10.1103/PhysRevLett.118.022005], the connected and leading disconnected hadronic light-by-light contributions to the muon anomalous magnetic moment (g -2 ) have been computed using lattice QCD ensembles corresponding to physical pion mass generated by the RBC/UKQCD Collaboration. However, the calculation is expected to suffer from a significant finite-volume error that scales like 1 /L2 where L is the spatial size of the lattice. In this paper, we demonstrate that this problem is cured by treating the muon and photons in infinite-volume, continuum QED, resulting in a weighting function that is precomputed and saved with affordable cost and sufficient accuracy. We present numerical results for the case when the quark loop is replaced by a muon loop, finding the expected exponential approach to the infinite volume limit and consistency with the known analytic result. We have implemented an improved weighting function which reduces both discretization and finite-volume effects arising from the hadronic part of the amplitude.

Using infinite-volume, continuum QED and lattice QCD for the hadronic light-by-light contribution to the muon anomalous magnetic moment

DOE PAGES

Blum, Thomas; Christ, Norman; Hayakawa, Masashi; ...

2017-08-22

In our previous work, the connected and leading disconnected hadronic light-by-light contributions to the muon anomalous magnetic moment (g — 2) have been computed using lattice QCD ensembles corresponding to physical pion mass generated by the RBC/UKQCD Collaboration. However, the calculation is expected to suffer from a significant finite-volume error that scales like 1/L 2 where L is the spatial size of the lattice. In this paper, we demonstrate that this problem is cured by treating the muon and photons in infinite-volume, continuum QED, resulting in a weighting function that is precomputed and saved with affordable cost and sufficient accuracy.more » We present numerical results for the case when the quark loop is replaced by a muon loop, finding the expected exponential approach to the infinite volume limit and consistency with the known analytic result. Here, we have implemented an improved weighting function which reduces both discretization and finite-volume effects arising from the hadronic part of the amplitude.« less

Using infinite-volume, continuum QED and lattice QCD for the hadronic light-by-light contribution to the muon anomalous magnetic moment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blum, Thomas; Christ, Norman; Hayakawa, Masashi

In our previous work, the connected and leading disconnected hadronic light-by-light contributions to the muon anomalous magnetic moment (g — 2) have been computed using lattice QCD ensembles corresponding to physical pion mass generated by the RBC/UKQCD Collaboration. However, the calculation is expected to suffer from a significant finite-volume error that scales like 1/L 2 where L is the spatial size of the lattice. In this paper, we demonstrate that this problem is cured by treating the muon and photons in infinite-volume, continuum QED, resulting in a weighting function that is precomputed and saved with affordable cost and sufficient accuracy.more » We present numerical results for the case when the quark loop is replaced by a muon loop, finding the expected exponential approach to the infinite volume limit and consistency with the known analytic result. Here, we have implemented an improved weighting function which reduces both discretization and finite-volume effects arising from the hadronic part of the amplitude.« less

Importance of proper renormalization scale-setting for QCD testing at colliders

DOE PAGES

Wu, Xing -Gang; Wang, Sheng -Quan; Brodsky, Stanley J.

2015-12-22

A primary problem affecting perturbative quantum chromodynamic (pQCD) analyses is the lack of a method for setting the QCD running-coupling renormalization scale such that maximally precise fixed-order predictions for physical observables are obtained. The Principle of Maximum Conformality (PMC) eliminates the ambiguities associated with the conventional renormalization scale-setting procedure, yielding predictions that are independent of the choice of renormalization scheme. The QCD coupling scales and the effective number of quark flavors are set order-by-order in the pQCD series. The PMC has a solid theoretical foundation, satisfying the standard renormalization group invariance condition and all of the self-consistency conditions derived frommore » the renormalization group. The PMC scales at each order are obtained by shifting the arguments of the strong force coupling constant αs to eliminate all non-conformal {βi} terms in the pQCD series. The {βi} terms are determined from renormalization group equations without ambiguity. The correct behavior of the running coupling at each order and at each phase-space point can then be obtained. The PMC reduces in the N C → 0 Abelian limit to the Gell-Mann-Low method. In this brief report, we summarize the results of our recent application of the PMC to a number of collider processes, emphasizing the generality and applicability of this approach. A discussion of hadronic Z decays shows that, by applying the PMC, one can achieve accurate predictions for the total and separate decay widths at each order without scale ambiguities. We also show that, if one employs the PMC to determine the top-quark pair forward-backward asymmetry at the next-to-next-to-leading order level, one obtains a comprehensive, self-consistent pQCD explanation for the Tevatron measurements of the asymmetry. This accounts for the “increasing-decreasing” behavior observed by the D0 collaboration for increasing tt¯ invariant mass. At lower energies, the angular distributions of heavy quarks can be used to obtain a direct determination of the heavy quark potential. A discussion of the angular distributions of massive quarks and leptons is also presented, including the fermionic component of the two-loop corrections to the electromagnetic form factors. Furthermore, these results demonstrate that the application of the PMC systematically eliminates a major theoretical uncertainty for pQCD predictions, thus increasing collider sensitivity to possible new physics beyond the Standard Model.« less

Study of ordered hadron chains with the ATLAS detector

DOE PAGES

Aaboud, M.; Aad, G.; Abbott, B.; ...

2017-11-29

The analysis of the momentum difference between charged hadrons in high-energy proton-proton collisions is performed in order to study coherent particle production. The observed correlation pattern agrees with a model of a helical QCD string fragmenting into a chain of ground-state hadrons. A threshold momentum difference in the production of adjacent pairs of charged hadrons is observed, in agreement with model predictions. The presence of low-mass hadron chains also explains the emergence of charge-combination-dependent two-particle correlations commonly attributed to Bose-Einstein interference. Here, the data sample consists of 190 μb –1 of minimum-bias events collected with proton-proton collisions at a center-of-massmore » energy √s=7 TeV in the early low-luminosity data taking with the ATLAS detector at the LHC.« less

Wilson Lines and Webs in Higher-Order QCD

NASA Astrophysics Data System (ADS)

White, Chris D.

2018-03-01

Wilson lines have a number of uses in non-abelian gauge theories. A topical example in QCD is the description of radiation in the soft or collinear limit, which must often be resummed to all orders in perturbation theory. Correlators involving a pair of Wilson lines are known to exponentiate in terms of special Feynman diagrams called "webs". I will show how this language can be extended to an arbitrary number of Wilson lines, which introduces novel new combinatoric structures (web mixing matrices) of interest in their own right. I will also summarise recent results obtained from applying this formalism at three-loop order, before concluding with a list of open problems.

Next-to-leading order QCD corrections to the decay of Higgs to vector meson and Z boson

NASA Astrophysics Data System (ADS)

Sun, Qing-Feng; Wang, An-Min

2018-02-01

The exclusive decay of the Higgs boson to a vector meson (J/ψ or Υ(1S)) and Z boson is studied in this work. The decay amplitudes are separated into two parts in a gauge invariant manner. The first part comes from the direct coupling of the Higgs boson to the charm (bottom) quark and the other from the HZZ* or the loop-induced HZ γ* vertexes in the standard model. While the branching ratios from the direct channel are much smaller than those of the indirect channel, their interference terms give nontrivial contributions. We further calculate the QCD radiative corrections to both channels, which reduce the total branching ratios by around 20% for both (J/ψ or Υ(1S)) production. Our results provide a possible chance to check the SM predictions of the {{Hc}}\\bar{{{c}}}({{Hb}}\\bar{{{b}}}) coupling and to seek for hints of new physics at the High Luminosity LHC or future hadron colliders. Supported by National Natural Science Foundation of China (11375168)

Structural and sequencing analysis of local target DNA recognition by MLV integrase.

PubMed

Aiyer, Sriram; Rossi, Paolo; Malani, Nirav; Schneider, William M; Chandar, Ashwin; Bushman, Frederic D; Montelione, Gaetano T; Roth, Monica J

2015-06-23

Target-site selection by retroviral integrase (IN) proteins profoundly affects viral pathogenesis. We describe the solution nuclear magnetic resonance structure of the Moloney murine leukemia virus IN (M-MLV) C-terminal domain (CTD) and a structural homology model of the catalytic core domain (CCD). In solution, the isolated MLV IN CTD adopts an SH3 domain fold flanked by a C-terminal unstructured tail. We generated a concordant MLV IN CCD structural model using SWISS-MODEL, MMM-tree and I-TASSER. Using the X-ray crystal structure of the prototype foamy virus IN target capture complex together with our MLV domain structures, residues within the CCD α2 helical region and the CTD β1-β2 loop were predicted to bind target DNA. The role of these residues was analyzed in vivo through point mutants and motif interchanges. Viable viruses with substitutions at the IN CCD α2 helical region and the CTD β1-β2 loop were tested for effects on integration target site selection. Next-generation sequencing and analysis of integration target sequences indicate that the CCD α2 helical region, in particular P187, interacts with the sequences distal to the scissile bonds whereas the CTD β1-β2 loop binds to residues proximal to it. These findings validate our structural model and disclose IN-DNA interactions relevant to target site selection. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Chiral phase transition of three flavor QCD with nonzero magnetic field using standard staggered fermions

NASA Astrophysics Data System (ADS)

Tomiya, Akio; Ding, Heng-Tong; Mukherjee, Swagato; Schmidt, Christian; Wang, Xiao-Dan

2018-03-01

Lattice simulations for (2+1)-flavor QCD with external magnetic field demon-strated that the quark mass is one of the important parameters responsible for the (inverse) magnetic catalysis. We discuss the dependences of chiral condensates and susceptibilities, the Polyakov loop on the magnetic field and quark mass in three degenerate flavor QCD. The lattice simulations are performed using standard staggered fermions and the plaquette action with spatial sizes Nσ = 16 and 24 and a fixed temporal size Nτ = 4. The value of the quark masses are chosen such that the system undergoes a first order chiral phase transition and crossover with zero magnetic field. We find that in light mass regime, the quark chiral condensate undergoes magnetic catalysis in the whole temperature region and the phase transition tend to become stronger as the magnetic field increases. In crossover regime, deconfinement transition temperature is shifted by the magnetic field when quark mass ma is less than 0:4. The lattice cutoff effects are also discussed.

Multi-Regge kinematics and the moduli space of Riemann spheres with marked points

DOE PAGES

Del Duca, Vittorio; Druc, Stefan; Drummond, James; ...

2016-08-25

We show that scattering amplitudes in planar N = 4 Super Yang-Mills in multi-Regge kinematics can naturally be expressed in terms of single-valued iterated integrals on the moduli space of Riemann spheres with marked points. As a consequence, scattering amplitudes in this limit can be expressed as convolutions that can easily be computed using Stokes’ theorem. We apply this framework to MHV amplitudes to leading-logarithmic accuracy (LLA), and we prove that at L loops all MHV amplitudes are determined by amplitudes with up to L + 4 external legs. We also investigate non-MHV amplitudes, and we show that they canmore » be obtained by convoluting the MHV results with a certain helicity flip kernel. We classify all leading singularities that appear at LLA in the Regge limit for arbitrary helicity configurations and any number of external legs. In conclusion, we use our new framework to obtain explicit analytic results at LLA for all MHV amplitudes up to five loops and all non-MHV amplitudes with up to eight external legs and four loops.« less

Structural basis for nuclear import complex dissociation by RanGTP.

PubMed

Lee, Soo Jae; Matsuura, Yoshiyuki; Liu, Sai Man; Stewart, Murray

2005-06-02

Nuclear protein import is mediated mainly by the transport factor importin-beta that binds cytoplasmic cargo, most often via the importin-alpha adaptor, and then transports it through nuclear pore complexes. This active transport is driven by disassembly of the import complex by nuclear RanGTP. The switch I and II loops of Ran change conformation with nucleotide state, and regulate its interactions with nuclear trafficking components. Importin-beta consists of 19 HEAT repeats that are based on a pair of antiparallel alpha-helices (referred to as the A- and B-helices). The HEAT repeats stack to yield two C-shaped arches, linked together to form a helicoidal molecule that has considerable conformational flexibility. Here we present the structure of full-length yeast importin-beta (Kap95p or karyopherin-beta) complexed with RanGTP, which provides a basis for understanding the crucial cargo-release step of nuclear import. We identify a key interaction site where the RanGTP switch I loop binds to the carboxy-terminal arch of Kap95p. This interaction produces a change in helicoidal pitch that locks Kap95p in a conformation that cannot bind importin-alpha or cargo. We suggest an allosteric mechanism for nuclear import complex disassembly by RanGTP.

The two-mass contribution to the three-loop gluonic operator matrix element Agg,Q(3)

NASA Astrophysics Data System (ADS)

Ablinger, J.; Blümlein, J.; De Freitas, A.; Goedicke, A.; Schneider, C.; Schönwald, K.

2018-07-01

We calculate the two-mass QCD contributions to the massive operator matrix element Agg,Q at O (αs3) in analytic form in Mellin N- and z-space, maintaining the complete dependence on the heavy quark mass ratio. These terms are important ingredients for the matching relations of the variable flavor number scheme in the presence of two heavy quark flavors, such as charm and bottom. In Mellin N-space the result is given in the form of nested harmonic, generalized harmonic, cyclotomic and binomial sums, with arguments depending on the mass ratio. The Mellin inversion of these quantities to z-space gives rise to generalized iterated integrals with square root valued letters in the alphabet, depending on the mass ratio as well. Numerical results are presented.

NMR and Bioinformatics Discovery of Exosites That Tune Metalloelastase Specificity for Solubilized Elastin and Collagen Triple Helices*

PubMed Central

Palmier, Mark O.; Fulcher, Yan G.; Bhaskaran, Rajagopalan; Duong, Vinh Q.; Fields, Gregg B.; Van Doren, Steven R.

2010-01-01

The catalytic domain of metalloelastase (matrix metalloproteinase-12 or MMP-12) is unique among MMPs in exerting high proteolytic activity upon fibrils that resist hydrolysis, especially elastin from lungs afflicted with chronic obstructive pulmonary disease or arteries with aneurysms. How does the MMP-12 catalytic domain achieve this specificity? NMR interface mapping suggests that α-elastin species cover the primed subsites, a strip across the β-sheet from β-strand IV to the II–III loop, and a broad bowl from helix A to helix C. The many contacts may account for the comparatively high affinity, as well as embedding of MMP-12 in damaged elastin fibrils in vivo. We developed a strategy called BINDSIght, for bioinformatics and NMR discovery of specificity of interactions, to evaluate MMP-12 specificity without a structure of a complex. BINDSIght integration of the interface mapping with other ambiguous information from sequences guided choice mutations in binding regions nearer the active site. Single substitutions at each of ten locations impair specific activity toward solubilized elastin. Five of them impair release of peptides from intact elastin fibrils. Eight lesions also impair specific activity toward triple helices from collagen IV or V. Eight sites map to the “primed” side in the III–IV, V–B, and S1′ specificity loops. Two map to the “unprimed” side in the IV–V and B–C loops. The ten key residues circumscribe the catalytic cleft, form an exosite, and are distinctive features available for targeting by new diagnostics or therapeutics. PMID:20663866

Improving RNA nearest neighbor parameters for helices by going beyond the two-state model.

PubMed

Spasic, Aleksandar; Berger, Kyle D; Chen, Jonathan L; Seetin, Matthew G; Turner, Douglas H; Mathews, David H

2018-06-01

RNA folding free energy change nearest neighbor parameters are widely used to predict folding stabilities of secondary structures. They were determined by linear regression to datasets of optical melting experiments on small model systems. Traditionally, the optical melting experiments are analyzed assuming a two-state model, i.e. a structure is either complete or denatured. Experimental evidence, however, shows that structures exist in an ensemble of conformations. Partition functions calculated with existing nearest neighbor parameters predict that secondary structures can be partially denatured, which also directly conflicts with the two-state model. Here, a new approach for determining RNA nearest neighbor parameters is presented. Available optical melting data for 34 Watson-Crick helices were fit directly to a partition function model that allows an ensemble of conformations. Fitting parameters were the enthalpy and entropy changes for helix initiation, terminal AU pairs, stacks of Watson-Crick pairs and disordered internal loops. The resulting set of nearest neighbor parameters shows a 38.5% improvement in the sum of residuals in fitting the experimental melting curves compared to the current literature set.

Crystal structure of bovine Cu,Zn superoxide dismutase at 3 A resolution: chain tracing and metal ligands.

PubMed Central

Richardson, J; Thomas, K A; Rubin, B H; Richardson, D C

1975-01-01

An electron density map at 3 angstrom resolution has been calculated for Cu2+, Zn2+ superoxide dismutase from bovine erythrocytes, and the course of the main chain has been traced. The dominant structural feature is an 8-stranded barrel of antiparallel beta-pleated sheet. There is one very short helical section and two long loops of non-repetitive structure. The Cu and Zn are bound between the loops and one side of the beta barrel and are about 6 Angstrom apart, with a common histidine ligand. The Cu has four histidine ligands in a somewhat distorted square plane, and the Zn has three histidines and an aspartate in approximately tetrahedral arrangement. The two coppers of a dimer are about 34 Angstrom apart. The two subunits have essentially the same conformation and have an extensive contact area that mainly involves hydrophobic side chain interactions. The overall folding pattern of the polypeptide chain is very similar to that of an immunoglobulin domain. Images PMID:1055410

The 1.25 Å resolution structure of phosphoribosyl-ATP pyrophosphohydrolase from Mycobacterium tuberculosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Javid-Majd, Farah; Yang, Dong; Ioerger, Thomas R.

2008-06-01

The crystal structure of M. tuberculosis phosphoribosyl-ATP pyrophosphohydrolase, the second enzyme in the histidine-biosynthetic pathway, is presented. The structural and inferred functional relationships between M. tuberculosis phosphoribosyl-ATP pyrophosphohydrolase and other members of the nucleoside-triphosphate pyrophosphatase-fold family are described. Phosphoribosyl-ATP pyrophosphohydrolase is the second enzyme in the histidine-biosynthetic pathway, irreversibly hydrolyzing phosphoribosyl-ATP to phosphoribosyl-AMP and pyrophosphate. It is encoded by the hisE gene, which is present as a separate gene in many bacteria and archaea but is fused to hisI in other bacteria, fungi and plants. Because of its essentiality for growth in vitro, HisE is a potential drug target formore » tuberculosis. The crystal structures of two native (uncomplexed) forms of HisE from Mycobacterium tuberculosis have been determined to resolutions of 1.25 and 1.79 Å. The structure of the apoenzyme reveals that the protein is composed of five α-helices with connecting loops and is a member of the α-helical nucleoside-triphosphate pyrophosphatase superfamily. The biological unit of the protein is a homodimer, with an active site on each subunit composed of residues exclusively from that subunit. A comparison with the Campylobacter jejuni dUTPase active site allowed the identification of putative metal- and substrate-binding sites in HisE, including four conserved glutamate and glutamine residues in the sequence that are consistent with a motif for pyrophosphohydrolase activity. However, significant differences between family members are observed in the loop region between α-helices H1 and H3. The crystal structure of M. tuberculosis HisE provides insights into possible mechanisms of substrate binding and the diversity of the nucleoside-triphosphate pyrophosphatase superfamily.« less

Holographic CBK relation

NASA Astrophysics Data System (ADS)

Gabadadze, Gregory; Tukhashvili, Giorgi

2018-07-01

The Crewther-Broadhurst-Kataev (CBK) relation connects the Bjorken function for deep-inelastic sum rules (or the Gross-Llewellyn Smith function) with the Adler function for electron-positron annihilation in QCD; it has been checked to hold up to four loops in perturbation theory. Here we study non-perturbative terms in the CBK relation using a holographic dual theory that is believed to capture properties of QCD. We show that for the large invariant momenta the perturbative CBK relation is exactly satisfied. For the small momenta non-perturbative corrections enter the relation and we calculate their significant effects. We also give an exact holographic expression for the Bjorken function, as well as for the entire three-point axial-vector-vector correlation function, and check their consistency in the conformal limit.

QCD Coupling from a Nonperturbative Determination of the Three-Flavor Λ Parameter.

PubMed

Bruno, Mattia; Brida, Mattia Dalla; Fritzsch, Patrick; Korzec, Tomasz; Ramos, Alberto; Schaefer, Stefan; Simma, Hubert; Sint, Stefan; Sommer, Rainer

2017-09-08

We present a lattice determination of the Λ parameter in three-flavor QCD and the strong coupling at the Z pole mass. Computing the nonperturbative running of the coupling in the range from 0.2 to 70 GeV, and using experimental input values for the masses and decay constants of the pion and the kaon, we obtain Λ_{MS[over ¯]}^{(3)}=341(12)  MeV. The nonperturbative running up to very high energies guarantees that systematic effects associated with perturbation theory are well under control. Using the four-loop prediction for Λ_{MS[over ¯]}^{(5)}/Λ_{MS[over ¯]}^{(3)} yields α_{MS[over ¯]}^{(5)}(m_{Z})=0.11852(84).

Chiral and deconfinement phase transition in the Hamiltonian approach to QCD in Coulomb gauge

NASA Astrophysics Data System (ADS)

Reinhardt, H.; Vastag, P.

2016-11-01

The chiral and deconfinement phase transitions are investigated within the variational Hamiltonian approach to QCD in Coulomb gauge. The temperature β-1 is introduced by compactifying a spatial dimension. Thereby the whole temperature dependence is encoded in the vacuum state on the spatial manifold R2×S1(β ) . The chiral quark condensate and the dual quark condensate (dressed Polyakov loop) are calculated as a function of the temperature. From their inflection points the pseudocritical temperatures for the chiral and deconfinement crossover transitions are determined. Using the zero-temperature quark and gluon propagators obtained within the variational approach as input, we find 170 and 198 MeV, respectively, for the chiral and deconfinement transition.

Structural variations of single and tandem mismatches in RNA duplexes: a joint MD simulation and crystal structure database analysis.

PubMed

Halder, Sukanya; Bhattacharyya, Dhananjay

2012-10-04

Internal loops within RNA duplex regions are formed by single or tandem basepairing mismatches with flanking canonical Watson-Crick basepairs on both sides. They are the most common motif observed in RNA secondary structures and play integral functional and structural roles. In this report, we have studied the structural features of 1 × 1, 2 × 2, and 3 × 3 internal loops using all-atom molecular dynamics (MD) simulation technique with explicit solvent model. As MD simulation is intricately dependent on the choice of force-field and these are often rather approximate, we have used both the most popular force-fields for nucleic acids-CHARMM27 and AMBER94-for a comparative analysis. We find that tandem noncanonical basepairs forming 2 × 2 and 3 × 3 internal loops are considerably more stable than the single mismatches forming 1 × 1 internal loops, irrespective of the force field. We have also analyzed crystal structure database to study the conservation of these helical fragments in the corresponding sets of RNA structures. We observe that the nature of stability in MD simulations mimic their fluctuating natures in crystal data sets also, probably indicating reliable natures of both the force fields to reproduce experimental results. We also notice significant structural changes in the wobble G:U basepairs present in these double helical stretches, leading to a biphasic stability for these wobble pairs to release the deformational strains introduced by internal loops within duplex regions.

Plasma response to sustainment with imposed-dynamo current drive in HIT-SI and HIT-SI3

NASA Astrophysics Data System (ADS)

Hossack, A. C.; Jarboe, T. R.; Chandra, R. N.; Morgan, K. D.; Sutherland, D. A.; Penna, J. M.; Everson, C. J.; Nelson, B. A.

2017-07-01

The helicity injected torus—steady inductive (HIT-SI) program studies efficient, steady-state current drive for magnetic confinement plasmas using a novel experimental method. Stable, high-beta spheromaks have been sustained using steady, inductive current drive. Externally induced loop voltage and magnetic flux are oscillated together so that helicity and power injection are always positive, sustaining the edge plasma current indefinitely. Imposed-dynamo current drive (IDCD) theory further shows that the entire plasma current is sustained. The method is ideal for low aspect ratio, toroidal geometries with closed flux surfaces. Experimental studies of spheromak plasmas sustained with IDCD have shown stable magnetic profiles with evidence of pressure confinement. New measurements show coherent motion of a stable spheromak in response to the imposed perturbations. On the original device two helicity injectors were mounted on either side of the spheromak and the injected mode spectrum was predominantly n  =  1. Coherent, rigid motion indicates that the spheromak is stable and a lack of plasma-generated n  =  1 energy indicates that the maximum q is maintained below 1 during sustainment. Results from the HIT-SI3 device are also presented. Three inductive helicity injectors are mounted on one side of the spheromak flux conserver. Varying the relative injector phasing changes the injected mode spectrum which includes n  =  2, 3, and higher modes.

Three-dimensional prominence-hosting magnetic configurations: Creating a helical magnetic flux rope

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xia, C.; Keppens, R.; Guo, Y.

2014-01-10

The magnetic configuration hosting prominences and their surrounding coronal structure is a key research topic in solar physics. Recent theoretical and observational studies strongly suggest that a helical magnetic flux rope is an essential ingredient to fulfill most of the theoretical and observational requirements for hosting prominences. To understand flux rope formation details and obtain magnetic configurations suitable for future prominence formation studies, we here report on three-dimensional isothermal magnetohydrodynamic simulations including finite gas pressure and gravity. Starting from a magnetohydrostatic corona with a linear force-free bipolar magnetic field, we follow its evolution when introducing vortex flows around the mainmore » polarities and converging flows toward the polarity inversion line near the bottom of the corona. The converging flows bring the feet of different loops together at the polarity inversion line, where magnetic reconnection and flux cancellation happen. Inflow and outflow signatures of the magnetic reconnection process are identified, and thereby the newly formed helical loops wind around preexisting ones so that a complete flux rope grows and ascends. When a macroscopic flux rope is formed, we switch off the driving flows and find that the system relaxes to a stable state containing a helical magnetic flux rope embedded in an overlying arcade structure. A major part of the formed flux rope is threaded by dipped field lines that can stably support prominence matter, while the total mass of the flux rope is in the order of 4-5× 10{sup 14} g.« less

Thermodynamic characterization of a triple-helical three-way junction containing a Hoogsteen branch point.

PubMed

Hüsler, P L; Klump, H H

1995-09-10

We have designed a Hoogsteen (HG) triple-helical three-way junction (ternary complex) constructed from three 33-mer oligonucleotides based on the same subset of sequences used for the Watson-Crick (WC) triple-helical three-way junction, characterized previously (P. L. Hüsler and H. H. Klump (1994) Arch. Biochem. Biophys., 313, 29-38). The junction differs primarily in the assembly of the branch point and the ends of the arms. The three oligonucleotides can each fold into a WC hairpin, linked by a four-member cytosine loop, each containing a homo-pyrimidine 10-mer single-strand extension. On lowering the pH (between 6 and 4), the extensions mutually associate to one of the other hairpins via Hoogsteen (HG) hydrogen bonding. Collectively, this process results in the formation of the branch point and the triple-helical arms. The HG triple-helical three-way junction is characterized by gel electrophoresis, circular dichroism, uv melting, and differential scanning calorimetry. The junction undergoes thermal unfolding in two distinct temperature regions. In the temperature range 15 to 50 degrees C loss of HG base pairing results in the dissociation of the three-way junction. Between 55 and 95 degrees C the resulting hairpins undergo further successive unfolding. The overall calorimetric unfolding enthalpy and entropy changes associated with the loss of HG base pairing are approximately equal to the sum of the enthalpy and entropy changes associated with the dissociation of the HG base pairing in the isolated arms (170.6 kcal.mol-1; 540.1 cal.mol-1.K-1). It is apparent from these results that in the proximity of the branch point the structure is not perturb or strain. This result is contrary to the results obtained for the WC triple-helical three-way and for three-way junctions constructed from canonical double-helical DNA. Complete folding of the junction requires either high Na+ (600 mM) ion concentrations or 40-60 mM Mg2+.

N* Experiments and Their Impact on Strong QCD Physics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burkert, Volker D.

Here, I give a brief overview of experimental studies of the spectrum and the structure of the excited states of the nucleon and what we learn about their internal structure. The focus is on the effort to obtain a more complete picture of the light-quark baryon excitation spectrum employing electromagnetic beams, and on the study of the transition form factors and helicity amplitudes and their dependence on the size of the four-momentum transfer $Q^2$, especially on some of the most prominent resonances. These were obtained in pion and eta electroproduction experiments off proton targets.

N^* Experiments and Their Impact on Strong QCD Physics

NASA Astrophysics Data System (ADS)

Burkert, Volker D.

2018-07-01

I give a brief report on experimental studies of the spectrum and the structure of the excited states of the nucleon and what we learn about their internal structure. The focus is on the effort to obtain a more complete picture of the light-quark baryon excitation spectrum employing electromagnetic beams, and on the study of the transition form factors and helicity amplitudes an their dependence on the size of the four-momentum transfer Q^2, especially on some of the most prominent resonances. These were obtained in pion and eta electroproduction experiments off proton targets.

N* Experiments and Their Impact on Strong QCD Physics

DOE PAGES

Burkert, Volker D.

2018-04-23

Here, I give a brief overview of experimental studies of the spectrum and the structure of the excited states of the nucleon and what we learn about their internal structure. The focus is on the effort to obtain a more complete picture of the light-quark baryon excitation spectrum employing electromagnetic beams, and on the study of the transition form factors and helicity amplitudes and their dependence on the size of the four-momentum transfer $Q^2$, especially on some of the most prominent resonances. These were obtained in pion and eta electroproduction experiments off proton targets.

Structural and mechanistic insights into Mps1 kinase activation.

PubMed

Wang, Wei; Yang, Yuting; Gao, Yuefeng; Xu, Quanbin; Wang, Feng; Zhu, Songcheng; Old, William; Resing, Katheryn; Ahn, Natalie; Lei, Ming; Liu, Xuedong

2009-08-01

Mps1 is one of the several essential kinases whose activation is required for robust mitotic spindle checkpoint signalling. The activity of Mps1 is tightly regulated and increases dramatically during mitosis or in response to spindle damage. To understand the molecular mechanism underlying Mps1 regulation, we determined the crystal structure of the kinase domain of Mps1. The 2.7-A-resolution crystal structure shows that the Mps1 kinase domain adopts a unique inactive conformation. Intramolecular interactions between the key Glu residue in the C helix of the N-terminal lobe and the backbone amides in the catalytic loop lock the kinase in the inactive conformation. Autophosphorylation appears to be a priming event for kinase activation. We identified Mps1 autophosphorylation sites in the activation and the P+1 loops. Whereas activation loop autophosphorylation enhances kinase activity, autophosphorylation at the P+1 loop (T686) is associated with the active kinase. Mutation of T686 autophosphorylation site impairs both autophosphorylation and transphosphorylation. Furthermore, we demonstrated that phosphorylation of T676 may be a priming event for phosphorylation at T686. Finally, we identified two critical lysine residues in the loop between helices EF and F that are essential for substrate recruitment and maintaining high levels of kinase activity. Our studies reveal critical biochemical mechanisms for Mps1 kinase regulation.

Characterization of a native hammerhead ribozyme derived from schistosomes

PubMed Central

OSBORNE, EDITH M.; SCHAAK, JANELL E.; DEROSE, VICTORIA J.

2005-01-01

A recent re-examination of the role of the helices surrounding the conserved core of the hammerhead ribozyme has identified putative loop–loop interactions between stems I and II in native hammerhead sequences. These extended hammerhead sequences are more active at low concentrations of divalent cations than are minimal hammerheads. The loop–loop interactions are proposed to stabilize a more active conformation of the conserved core. Here, a kinetic and thermodynamic characterization of an extended hammerhead sequence derived from Schistosoma mansoni is performed. Biphasic kinetics are observed, suggesting the presence of at least two conformers, one cleaving with a fast rate and the other with a slow rate. Replacing loop II with a poly(U) sequence designed to eliminate the interaction between the two loops results in greatly diminished activity, suggesting that the loop–loop interactions do aid in forming a more active conformation. Previous studies with minimal hammerheads have shown deleterious effects of Rp-phosphorothioate substitutions at the cleavage site and 5′ to A9, both of which could be rescued with Cd2+. Here, phosphorothioate modifications at the cleavage site and 5′ to A9 were made in the schistosome-derived sequence. In Mg2+, both phosphorothioate substitutions decreased the overall fraction cleaved without significantly affecting the observed rate of cleavage. The addition of Cd2+ rescued cleavage in both cases, suggesting that these are still putative metal binding sites in this native sequence. PMID:15659358

Unveiling the proton spin decomposition at a future electron-ion collider

DOE PAGES

Aschenauer, Elke C.; Sassot, Rodolfo; Stratmann, Marco

2015-11-24

We present a detailed assessment of how well a future electron-ion collider could constrain helicity parton distributions in the nucleon and, therefore, unveil the role of the intrinsic spin of quarks and gluons in the proton’s spin budget. Any remaining deficit in this decomposition will provide the best indirect constraint on the contribution due to the total orbital angular momenta of quarks and gluons. Specifically, all our studies are performed in the context of global QCD analyses based on realistic pseudodata and in the light of the most recent data obtained from polarized proton-proton collisions at BNL-RHIC that have providedmore » evidence for a significant gluon polarization in the accessible, albeit limited range of momentum fractions. We also present projections on what can be achieved on the gluon’s helicity distribution by the end of BNL-RHIC operations. As a result, all estimates of current and projected uncertainties are performed with the robust Lagrange multiplier technique.« less

Fine flow structures in the transition region small-scale loops

NASA Astrophysics Data System (ADS)

Yan, L.; Peter, H.; He, J.; Wei, Y.

2016-12-01

The observation and model have suggested that the transition region EUV emission from the quiet sun region is contributed by very small scale loops which have not been resolved. Recently, the observation from IRIS has revealed that this kind of small scale loops. Based on the high resolution spectral and imaging observation from IRIS, much more detail work needs to be done to reveal the fine flow features in this kind of loop to help us understand the loop heating. Here, we present a detail statistical study of the spatial and temporal evolution of Si IV line profiles of small scale loops and report the spectral features: there is a transition from blue (red) wing enhancement dominant to red (blue) wing enhancement dominant along the cross-section of the loop, which is independent of time. This feature appears as the loop appear and disappear as the loop un-visible. This is probably the signature of helical flow along the loop. The result suggests that the brightening of this kind of loop is probably due to the current dissipation heating in the twisted magnetic field flux tube.

Crystal structure of four-stranded Oxytricha telomeric DNA

NASA Technical Reports Server (NTRS)

Kang, C.; Zhang, X.; Ratliff, R.; Moyzis, R.; Rich, A.

1992-01-01

The sequence d(GGGGTTTTGGGG) from the 3' overhang of the Oxytricha telomere has been crystallized and its three-dimensional structure solved to 2.5 A resolution. The oligonucleotide forms hairpins, two of which join to make a four-stranded helical structure with the loops containing four thymine residues at either end. The guanine residues are held together by cyclic hydrogen bonding and an ion is located in the centre. The four guanine residues in each segment have a glycosyl conformation that alternates between anti and syn. There are two four-stranded molecules in the asymmetric unit showing that the structure has some intrinsic flexibility.

Power counting and modes in SCET

NASA Astrophysics Data System (ADS)

Goerke, Raymond; Luke, Michael

2018-02-01

We present a formulation of soft-collinear effective theory (SCET) in the two-jet sector as a theory of decoupled sectors of QCD coupled to Wilson lines. The formulation is manifestly boost-invariant, does not require the introduction of ultrasoft modes at the hard matching scale Q, and has manifest power counting in inverse powers of Q. The spurious infrared divergences which arise in SCET when ultrasoft modes are not included in loops disappear when the overlap between the sectors is correctly subtracted, in a manner similar to the familiar zero-bin subtraction of SCET. We illustrate this approach by analyzing deep inelastic scattering in the endpoint region in SCET and comment on other applications.

Flux tubes in the SU(3) vacuum: London penetration depth and coherence length

NASA Astrophysics Data System (ADS)

Cea, Paolo; Cosmai, Leonardo; Cuteri, Francesca; Papa, Alessandro

2014-05-01

Within the dual superconductor scenario for the QCD confining vacuum, the chromoelectric field generated by a static qq¯ pair can be fitted by a function derived, by dual analogy, from a simple variational model for the magnitude of the normalized order parameter of an isolated Abrikosov vortex. Previous results for the SU(3) vacuum are revisited, but here the transverse chromoelectric field is measured by means of the connected correlator of two Polyakov loops and, in order to reduce noise, the smearing procedure is used instead of cooling. The penetration and coherence lengths of the flux tube are then extracted from the fit and compared with previous results.

Dimension-5 C P -odd operators: QCD mixing and renormalization

DOE PAGES

Bhattacharya, Tanmoy; Cirigliano, Vincenzo; Gupta, Rajan; ...

2015-12-23

Here, we study the off-shell mixing and renormalization of flavor-diagonal dimension-five T- and P-odd operators involving quarks, gluons, and photons, including quark electric dipole and chromoelectric dipole operators. Furthermore, we present the renormalization matrix to one loop in themore » $$\\bar{MS}$$ scheme. We also provide a definition of the quark chromoelectric dipole operator in a regularization-independent momentum-subtraction scheme suitable for nonperturbative lattice calculations and present the matching coefficients with the $$\\bar{MS}$$ scheme to one loop in perturbation theory, using both the naïve dimensional regularization and ’t Hooft–Veltman prescriptions for γ 5.« less

Interquark potential with finite quark mass from lattice QCD.

PubMed

Kawanai, Taichi; Sasaki, Shoichi

2011-08-26

We present an investigation of the interquark potential determined from the q ̄q Bethe-Salpeter (BS) amplitude for heavy quarkonia in lattice QCD. The q ̄q potential at finite quark mass m(q) can be calculated from the equal-time and Coulomb gauge BS amplitude through the effective Schrödinger equation. The definition of the potential itself requires information about a kinetic mass of the quark. We then propose a self-consistent determination of the quark kinetic mass on the same footing. To verify the proposed method, we perform quenched lattice QCD simulations with a relativistic heavy-quark action at a lattice cutoff of 1/a≈2.1  GeV in a range 1.0≤m(q)≤3.6 GeV. Our numerical results show that the q ̄q potential in the m(q)→∞ limit is fairly consistent with the conventional one obtained from Wilson loops. The quark-mass dependence of the q ̄q potential and the spin-spin potential are also examined. © 2011 American Physical Society

Baryon mass splittings and strong CP violation in SU(3) chiral perturbation theory

DOE PAGES

de Vries, Jordy; Mereghetti, Emanuele; Walker-Loud, Andre P.

2015-10-08

We study SU(3) flavor breaking corrections to the relation between the octet baryon masses and the nucleon-meson CP-violating interactions induced by the QCD theta term. We also work within the framework of SU(3) chiral perturbation theory and work through next-to-next-to-leading order in the SU(3) chiral expansion, which is O(m 2 q). At lowest order, the CP-odd couplings induced by the QCD θ - term are determined by mass splittings of the baryon octet, the classic result of Crewther et al. We show that for each isospin-invariant CP-violating nucleon-meson interaction there exists one relation which is respected by loop corrections upmore » to the order we work, while other leading-order relations are violated. With these relations we extract a precise value of the pion-nucleon coupling g - 0 by using recent lattice QCD evaluations of the proton-neutron mass splitting. Additionally, we derive semi-precise values for CP-violating coupling constants between heavier mesons and nucleons and discuss their phenomenological impact on electric dipole moments of nucleons and nuclei.« less

Baryon mass splittings and strong CP violation in SU(3) chiral perturbation theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

de Vries, Jordy; Mereghetti, Emanuele; Walker-Loud, Andre P.

We study SU(3) flavor breaking corrections to the relation between the octet baryon masses and the nucleon-meson CP-violating interactions induced by the QCD theta term. We also work within the framework of SU(3) chiral perturbation theory and work through next-to-next-to-leading order in the SU(3) chiral expansion, which is O(m 2 q). At lowest order, the CP-odd couplings induced by the QCD θ - term are determined by mass splittings of the baryon octet, the classic result of Crewther et al. We show that for each isospin-invariant CP-violating nucleon-meson interaction there exists one relation which is respected by loop corrections upmore » to the order we work, while other leading-order relations are violated. With these relations we extract a precise value of the pion-nucleon coupling g - 0 by using recent lattice QCD evaluations of the proton-neutron mass splitting. Additionally, we derive semi-precise values for CP-violating coupling constants between heavier mesons and nucleons and discuss their phenomenological impact on electric dipole moments of nucleons and nuclei.« less

Persistence of evolutionary memory: primordial six-transmembrane helical domain mu opiate receptors selectively linked to endogenous morphine signaling.

PubMed

Kream, Richard M; Sheehan, Melinda; Cadet, Patrick; Mantione, Kirk J; Zhu, Wei; Casares, Federico; Stefano, George B

2007-12-01

Biochemical, molecular and pharmacological evidence for two unique six-transmembrane helical (TMH) domain opiate receptors expressed from the micro opioid receptor (MOR) gene have been shown. Designated micro3 and micro4 receptors, both protein species are Class A rhodopsin-like members of the superfamily of G-protein coupled receptors but are selectively tailored to mediate the cellular regulatory effects of endogenous morphine and related morphinan alkaloids via stimulation of nitric oxide (NO) production and release. Both micro3 and micro4 receptors lack an amino acid sequence of approximately 90 amino acids that constitute the extracellular N-terminal and TMH1 domains and part of the first intracellular loop of the micro1 receptor, but retain the empirically defined ligand binding pocket distributed across conserved TMH2, TMH3, and TMH7 domains of the micro1 sequence. Additionally, the receptor proteins are terminated by unique intracellular C-terminal amino acid sequences that serve as putative coupling or docking domains required for constitutive NO synthase activation. Because the recognition profile of micro3 and micro4 receptors is restricted to rigid benzylisoquinoline alkaloids typified by morphine and its extended family of chemical congeners, it is hypothesized that conformational stabilization provided by interaction of extended extracellular N-terminal protein domains and the extracellular loops is required for binding of endogenous opioid peptides as well as synthetic flexible opiate alkaloids.

Crystal Structure of FadA Adhesin from Fusobacterium nucleatum Reveals a Novel Oligomerization Motif, the Leucine Chain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nithianantham, Stanley; Xu, Minghua; Yamada, Mitsunori

2009-04-07

Many bacterial appendages have filamentous structures, often composed of repeating monomers assembled in a head-to-tail manner. The mechanisms of such linkages vary. We report here a novel protein oligomerization motif identified in the FadA adhesin from the Gram-negative bacterium Fusobacterium nucleatum. The 2.0 {angstrom} crystal structure of the secreted form of FadA (mFadA) reveals two antiparallel {alpha}-helices connected by an intervening 8-residue hairpin loop. Leucine-leucine contacts play a prominent dual intra- and intermolecular role in the structure and function of FadA. First, they comprise the main association between the two helical arms of the monomer; second, they mediate the head-to-tailmore » association of monomers to form the elongated polymers. This leucine-mediated filamentous assembly of FadA molecules constitutes a novel structural motif termed the 'leucine chain.' The essential role of these residues in FadA is corroborated by mutagenesis of selected leucine residues, which leads to the abrogation of oligomerization, filament formation, and binding to host cells.« less

Three dimensional equilibrium solutions for a current-carrying reversed-field pinch plasma with a close-fitting conducting shell

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koliner, J. J.; Boguski, J., E-mail: boguski@wisc.edu; Anderson, J. K.

2016-03-15

In order to characterize the Madison Symmetric Torus (MST) reversed-field pinch (RFP) plasmas that bifurcate to a helical equilibrium, the V3FIT equilibrium reconstruction code was modified to include a conducting boundary. RFP plasmas become helical at a high plasma current, which induces large eddy currents in MST's thick aluminum shell. The V3FIT conducting boundary accounts for the contribution from these eddy currents to external magnetic diagnostic coil signals. This implementation of V3FIT was benchmarked against MSTFit, a 2D Grad-Shafranov solver, for axisymmetric plasmas. The two codes both fit B{sub θ} measurement loops around the plasma minor diameter with qualitative agreementmore » between each other and the measured field. Fits in the 3D case converge well, with q-profile and plasma shape agreement between two distinct toroidal locking phases. Greater than 60% of the measured n = 5 component of B{sub θ} at r = a is due to eddy currents in the shell, as calculated by the conducting boundary model.« less

Three dimensional equilibrium solutions for a current-carrying reversed-field pinch plasma with a close-fitting conducting shell

DOE PAGES

Koliner, J. J.; Boguski, J.; Anderson, J. K.; ...

2016-03-25

In order to characterize the Madison Symmetric Torus (MST) reversed-field pinch(RFP)plasmas that bifurcate to a helical equilibrium, the V3FIT equilibrium reconstruction code was modified to include a conducting boundary. RFPplasmas become helical at a high plasma current, which induces large eddy currents in MST's thick aluminum shell. The V3FIT conducting boundary accounts for the contribution from these eddy currents to external magnetic diagnostic coil signals. This implementation of V3FIT was benchmarked against MSTFit, a 2D Grad-Shafranov solver, for axisymmetric plasmas. The two codes both fit B measurement loops around the plasma minor diameter with qualitative agreement between each other andmore » the measured field. Fits in the 3D case converge well, with q-profile and plasma shape agreement between two distinct toroidal locking phases. Greater than 60% of the measured n = 5 component of B at r = a is due to eddy currents in the shell, as calculated by the conducting boundary model.« less

Structure of Arabidopsis thaliana Rubisco activase.

PubMed

Hasse, Dirk; Larsson, Anna M; Andersson, Inger

2015-04-01

The CO2-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is inactivated by the formation of dead-end complexes with inhibitory sugar phosphates. In plants and green algae, the ATP-dependent motor protein Rubisco activase restores catalytic competence by facilitating conformational changes in Rubisco that promote the release of the inhibitory compounds from the active site. Here, the crystal structure of Rubisco activase from Arabidopsis thaliana is presented at 2.9 Å resolution. The structure reveals an AAA+ two-domain structure. More than 100 residues in the protein were not visible in the electron-density map owing to conformational disorder, but were verified to be present in the crystal by mass spectrometry. Two sulfate ions were found in the structure. One was bound in the loop formed by the Walker A motif at the interface of the domains. A second sulfate ion was bound at the N-terminal end of the first helix of the C-terminal domain. The protein packs in a helical fashion in the crystal, as observed previously for Rubisco activase, but differences in the helical pitch indicate flexibility in the packing of the protein.

Bulk viscous corrections to screening and damping in QCD at high temperatures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Du, Qianqian; Dumitru, Adrian; Guo, Yun

2017-01-01

Non-equilibrium corrections to the distribution functions of quarks and gluons in a hot and dense QCD medium modify the \\hard thermal loops" (HTL). The HTLs determine the retarded, advanced, and symmetric (time-ordered) propagators for gluons with soft momenta as well as the Debye screening and Landau damping mass scales. Here, we compute such corrections to a thermal as well as to a non-thermal fixed point. The screening and damping mass scales are sensitive to the bulk pressure and hence to (pseudo-) critical dynamical scaling of the bulk viscosity in the vicinity of a second-order critical point. This could be reectedmore » in the properties of quarkonium bound states in the deconfined phase and in the dynamics of soft gluon fields.« less

Nonperturbative renormalization of the axial current in Nf=3 lattice QCD with Wilson fermions and a tree-level improved gauge action

NASA Astrophysics Data System (ADS)

Bulava, John; Della Morte, Michele; Heitger, Jochen; Wittemeier, Christian

2016-06-01

We nonperturbatively determine the renormalization factor of the axial vector current in lattice QCD with Nf=3 flavors of Wilson-clover fermions and the tree-level Symanzik-improved gauge action. The (by now standard) renormalization condition is derived from the massive axial Ward identity, and it is imposed among Schrödinger functional states with large overlap on the lowest lying hadronic state in the pseudoscalar channel, in order to reduce kinematically enhanced cutoff effects. We explore a range of couplings relevant for simulations at lattice spacings of ≈0.09 fm and below. An interpolation formula for ZA(g02) , smoothly connecting the nonperturbative values to the 1-loop expression, is provided together with our final results.

Hyper-scaling relations in the conformal window from dynamic AdS/QCD

NASA Astrophysics Data System (ADS)

Evans, Nick; Scott, Marc

2014-09-01

Dynamic AdS/QCD is a holographic model of strongly coupled gauge theories with the dynamics included through the running anomalous dimension of the quark bilinear, γ. We apply it to describe the physics of massive quarks in the conformal window of SU(Nc) gauge theories with Nf fundamental flavors, assuming the perturbative two-loop running for γ. We show that to find regular, holographic renormalization group flows in the infrared, the decoupling of the quark flavors at the scale of the mass is important, and enact it through suitable boundary conditions when the flavors become on shell. We can then compute the quark condensate and the mesonic spectrum (Mρ,Mπ,Mσ) and decay constants. We compute their scaling dependence on the quark mass for a number of examples. The model matches perturbative expectations for large quark mass and naïve dimensional analysis (including the anomalous dimensions) for small quark mass. The model allows study of the intermediate regime where there is an additional scale from the running of the coupling, and we present results for the deviation of scalings from assuming only the single scale of the mass.

Enzymatically cross-linked tilapia gelatin hydrogels: physical, chemical, and hybrid networks.

PubMed

Bode, Franziska; da Silva, Marcelo Alves; Drake, Alex F; Ross-Murphy, Simon B; Dreiss, Cécile A

2011-10-10

This Article investigates different types of networks formed from tilapia fish gelatin (10% w/w) in the presence and absence of the enzymatic cross-linker microbial transglutaminase. The influence of the temperature protocol and cross-linker concentration (0-55 U mTGase/g gelatin) was examined in physical, chemical, and hybrid gels, where physical gels arise from the formation of triple helices that act as junction points when the gels are cooled below the gelation point. A combination of rheology and optical rotation was used to study the evolution of the storage modulus (G') over time and the number of triple helices formed for each type of gel. We attempted to separate the final storage modulus of the gels into its chemical and physical contributions to examine the existence or otherwise of synergism between the two types of networks. Our experiments show that the gel characteristics vary widely with the thermal protocol. The final storage modulus in chemical gels increased with enzyme concentration, possibly due to the preferential formation of closed loops at low cross-linker amount. In chemical-physical gels, where the physical network (helices) was formed consecutively to the covalent one, we found that below a critical enzyme concentration the more extensive the chemical network is (as measured by G'), the weaker the final gel is. The storage modulus attributed to the physical network decreased exponentially as a function of G' from the chemical network, but both networks were found to be purely additive. Helices were not thermally stabilized. The simultaneous formation of physical and chemical networks (physical-co-chemical) resulted in G' values higher than the individual networks formed under the same conditions. Two regimes were distinguished: at low enzyme concentration (10-20 U mTGase/g gelatin), the networks were formed in series, but the storage modulus from the chemical network was higher in the presence of helices (compared to pure chemical gels); at higher enzyme concentration (30-40 U mTGase/g gelatin), strong synergistic effects were found as a large part of the covalent network became ineffective upon melting of the helices.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buras, Andrzej J.; /Munich, Tech. U.; Gorbahn, Martin

The authors calculate the complete next-to-next-to-leading order QCD corrections to the charm contribution of the rare decay K{sup +} {yields} {pi}{sup +}{nu}{bar {nu}}. They encounter several new features, which were absent in lower orders. They discuss them in detail and present the results for the two-loop matching conditions of the Wilson coefficients, the three-loop anomalous dimensions, and the two-loop matrix elements of the relevant operators that enter the next-to-next-to-leading order renormalization group analysis of the Z-penguin and the electroweak box contribution. The inclusion of the next-to-next-to-leading order QCD corrections leads to a significant reduction of the theoretical uncertainty from {+-}more » 9.8% down to {+-} 2.4% in the relevant parameter P{sub c}(X), implying the leftover scale uncertainties in {Beta}(K{sup +} {yields} {pi}{sup +}{nu}{bar {nu}}) and in the determination of |V{sub td}|, sin 2{beta}, and {gamma} from the K {yields} {pi}{nu}{bar {nu}} system to be {+-} 1.3%, {+-} 1.0%, {+-} 0.006, and {+-} 1.2{sup o}, respectively. For the charm quark {ovr MS} mass m{sub c}(m{sub c}) = (1.30 {+-} 0.05) GeV and |V{sub us}| = 0.2248 the next-to-leading order value P{sub c}(X) = 0.37 {+-} 0.06 is modified to P{sub c}(X) = 0.38 {+-} 0.04 at the next-to-next-to-leading order level with the latter error fully dominated by the uncertainty in m{sub c}(m{sub c}). They present tables for P{sub c}(X) as a function of m{sub c}(m{sub c}) and {alpha}{sub s}(M{sub z}) and a very accurate analytic formula that summarizes these two dependences as well as the dominant theoretical uncertainties. Adding the recently calculated long-distance contributions they find {Beta}(K{sup +} {yields} {pi}{sup +}{nu}{bar {nu}}) = (8.0 {+-} 1.1) x 10{sup -11} with the present uncertainties in m{sub c}(m{sub c}) and the Cabibbo-Kobayashi-Maskawa elements being the dominant individual sources in the quoted error. They also emphasize that improved calculations of the long-distance contributions to K{sup +} {yields} {pi}{sup +}{nu}{bar {nu}} and of the isospin breaking corrections in the evaluation of the weak current matrix elements from K{sup +} {yields} {pi}{sup 0}e{sup +}{nu} would be valuable in order to increase the potential of the two golden K {yields} {pi}{nu}{bar {nu}} decays in the search for new physics.« less

Constituent Quarks and Gluons, Polyakov loop and the Hadron Resonance Gas Model ***

NASA Astrophysics Data System (ADS)

Megías, E.; Ruiz Arriola, E.; Salcedo, L. L.

2014-03-01

Based on first principle QCD arguments, it has been argued in [1] that the vacuum expectation value of the Polyakov loop can be represented in the hadron resonance gas model. We study this within the Polyakov-constituent quark model by implementing the quantum and local nature of the Polyakov loop [2, 3]. The existence of exotic states in the spectrum is discussed. Presented by E. Megías at the International Nuclear Physics Conference INPC 2013, 2-7 June 2013, Firenze, Italy.Supported by Plan Nacional de Altas Energías (FPA2011-25948), DGI (FIS2011-24149), Junta de Andalucía grant FQM-225, Spanish Consolider-Ingenio 2010 Programme CPAN (CSD2007-00042), Spanish MINECO's Centro de Excelencia Severo Ochoa Program grant SEV-2012-0234, and the Juan de la Cierva Program.

Expanded turn conformations: characterization and sequence-structure correspondence in alpha-turns with implications in helix folding.

PubMed

Dasgupta, Bhaskar; Pal, Lipika; Basu, Gautam; Chakrabarti, Pinak

2004-05-01

Like the beta-turns, which are characterized by a limiting distance between residues two positions apart (i, i+3), a distance criterion (involving residues at positions i and i+4) is used here to identify alpha-turns from a database of known protein structures. At least 15 classes of alpha-turns have been enumerated based on the location in the phi,psi space of the three central residues (i+1 to i+3)-one of the major being the class AAA, where the residues occupy the conventional helical backbone torsion angles. However, moving towards the C-terminal end of the turn, there is a shift in the phi,psi angles towards more negative phi, such that the electrostatic repulsion between two consecutive carbonyl oxygen atoms is reduced. Except for the last position (i+4), there is not much similarity in residue composition at different positions of hydrogen and non-hydrogen bonded AAA turns. The presence or absence of Pro at i+1 position of alpha- and beta-turns has a bearing on whether the turn is hydrogen-bonded or without a hydrogen bond. In the tertiary structure, alpha-turns are more likely to be found in beta-hairpin loops. The residue composition at the beginning of the hydrogen bonded AAA alpha-turn has similarity with type I beta-turn and N-terminal positions of helices, but the last position matches with the C-terminal capping position of helices, suggesting that the existence of a "helix cap signal" at i+4 position prevents alpha-turns from growing into helices. Our results also provide new insights into alpha-helix nucleation and folding. Copyright 2004 Wiley-Liss, Inc.

Spin-1 Particles and Perturbative QCD

NASA Astrophysics Data System (ADS)

de Melo, J. P. B. C.; Frederico, T.; Ji, Chueng-Ryong

2018-07-01

Due to the angular condition in the light-front dynamics (LFD), the extraction of the electromagnetic form factors for spin-1 particles can be uniquely determined taking into account implicitly non-valence and/or the zero-mode contributions to the matrix elements of the electromagnetic current. No matter which matrix elements of the electromagnetic current is used to extract the electromagnetic form factors, the same unique result is obtained. As physical observables, the electromagnetic form factors obtained from matrix elements of the current in LFD must be equal to those obtained in the instant form calculations. Recently, the Babar collaboration (Phys Rev D 78:071103, 2008) has analyzed the reaction e^+ + e^-→ ρ ^+ + ρ ^- at √{s}=10.58 GeV to measure the cross section as well as the ratios of the helicity amplitudes F_{λ 'λ }. We present our recent analysis of the Babar data for the rho meson considering the angular condition in LFD to put a stringent test on the onset of asymptotic perturbative QCD and predict the energy regime where the subleading contributions are still considerable.

Unsteady numerical analysis of solid-liquid two-phase flow in stirred tank with double helical ribbon impeller

NASA Astrophysics Data System (ADS)

Bai, He; Chen, Xiangshan; Zhao, Guangyu; Xiao, Chenglei; Li, Chen; Zhong, Cheng; Chen, Yu

2017-08-01

In order to enhance the mixing process of soil contaminated by oil and water, one kind of double helical ribbon (DHR) impeller was developed. In this study, the unsteady simulation analysis of solid-liquid two-phase flow in stirring tank with DHR impeller was conducted by the the computational fluid dynamics and the multi-reference frame (MRF) method. It was found that at 0-3.0 s stage, the rate of liquid was greater than the rate of solid particles, while the power consumption was 5-6 times more than the smooth operation. The rates of the liquid and the solid particles were almost the same, and the required power was 32 KW at t > 3.0 s. The flow of the solid particles in the tank was a typical axial circle flow, and the dispersed sequence of the solid that was accumulated at the bottom of the tank was: the bottom loop region, the annular region near the wall of the groove and finally the area near axial center. The results show that the DHR impeller was suitable for the mixing of liquid-solid two-phase.

Branching ratios, CP asymmetries and polarizations of B→ ψ (2S) V decays

NASA Astrophysics Data System (ADS)

Rui, Zhou; Li, Ya; Xiao, Zhen-Jun

2017-09-01

We analyze the non-leptonic decays B/B_s→ ψ (2S) V with V=(ρ , ω , K^{*}, φ ) by employing the perturbative QCD (pQCD) factorization approach. Here the branching ratios, the CP asymmetries and the complete set of polarization observables are investigated systematically. Besides the traditional contributions from the factorizable and non-factorizable diagrams at the leading order, the next-to-leading order (NLO) vertex corrections could also provide considerable contributions. The pQCD predictions for the branching ratios of the B_{(s)}→ ψ (2S)K^{*}, ψ (2S)φ decays are consistent with the measured values within errors. As for B→ ψ (2S) ρ , ψ (2S) ω decays, the branching ratios can reach the order of 10^{-5} and could be measured in the LHCb and Belle-II experiments. The numerical results show that the direct CP asymmetries of the considered decays are very small. Thus the observation of any large direct CP asymmetry for these decays will be a signal for new physics. The mixing-induced CP asymmetries in the neutral modes are very close to sin 2β _{(s)}, which suggests that these channels can give a cross-check on the measurement of the Cabbibo-Kobayashi-Maskawa (CKM) angle β and β _s. We find that the longitudinal polarization fractions f_0 are suppressed to ˜ 50% due to the large non-factorizable contributions. The magnitudes and phases of the two transverse amplitudes A_{allel } and A_{\\perp } are roughly equal, which is an indication for the approximate light-quark helicity conservation in these decays. The overall polarization observables of B→ ψ (2S) K^{*0} and B_s→ ψ (2S) φ channels are also in good agreement with the experimental measurements as reported by LHCb and BaBar. Other results can also be tested by the LHCb and Belle-II experiments.

Branching ratios, CP asymmetries and polarizations of $$B\\rightarrow \\psi (2S) V$$ decays

DOE PAGES

Rui, Zhou; Li, Ya; Xiao, Zhen -Jun

2017-09-14

We analyze the non-leptonic decays B/B s→ψ(2S)V with V=(ρ,ω,K*,Φ) by employing the perturbative QCD (pQCD) factorization approach. Here the branching ratios, the CP asymmetries and the complete set of polarization observables are investigated systematically. Besides the traditional contributions from the factorizable and non-factorizable diagrams at the leading order, the next-to-leading order (NLO) vertex corrections could also provide considerable contributions. The pQCD predictions for the branching ratios of the B (s)→ψ(2S)K*,ψ(2S) decays are consistent with the measured values within errors. As for B→ψ(2S)ρ,ψ(2S)ω decays, the branching ratios can reach the order of 10 –5 and could be measured in the LHCbmore » and Belle-II experiments. The numerical results show that the direct CP asymmetries of the considered decays are very small. Thus the observation of any large direct CP asymmetry for these decays will be a signal for new physics. The mixing-induced CP asymmetries in the neutral modes are very close to sin2β (s), which suggests that these channels can give a cross-check on the measurement of the Cabbibo–Kobayashi–Maskawa (CKM) angle β and β s. We find that the longitudinal polarization fractions f 0 are suppressed to ~50% due to the large non-factorizable contributions. The magnitudes and phases of the two transverse amplitudes A∥ and A⊥ are roughly equal, which is an indication for the approximate light-quark helicity conservation in these decays. The overall polarization observables of B→ψ(2S)K* 0 and B s→ψ(2S)Φ channels are also in good agreement with the experimental measurements as reported by LHCb and BaBar. In conclusion, other results can also be tested by the LHCb and Belle-II experiments.« less

Branching ratios, CP asymmetries and polarizations of $$B\\rightarrow \\psi (2S) V$$ decays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rui, Zhou; Li, Ya; Xiao, Zhen -Jun

We analyze the non-leptonic decays B/B s→ψ(2S)V with V=(ρ,ω,K*,Φ) by employing the perturbative QCD (pQCD) factorization approach. Here the branching ratios, the CP asymmetries and the complete set of polarization observables are investigated systematically. Besides the traditional contributions from the factorizable and non-factorizable diagrams at the leading order, the next-to-leading order (NLO) vertex corrections could also provide considerable contributions. The pQCD predictions for the branching ratios of the B (s)→ψ(2S)K*,ψ(2S) decays are consistent with the measured values within errors. As for B→ψ(2S)ρ,ψ(2S)ω decays, the branching ratios can reach the order of 10 –5 and could be measured in the LHCbmore » and Belle-II experiments. The numerical results show that the direct CP asymmetries of the considered decays are very small. Thus the observation of any large direct CP asymmetry for these decays will be a signal for new physics. The mixing-induced CP asymmetries in the neutral modes are very close to sin2β (s), which suggests that these channels can give a cross-check on the measurement of the Cabbibo–Kobayashi–Maskawa (CKM) angle β and β s. We find that the longitudinal polarization fractions f 0 are suppressed to ~50% due to the large non-factorizable contributions. The magnitudes and phases of the two transverse amplitudes A∥ and A⊥ are roughly equal, which is an indication for the approximate light-quark helicity conservation in these decays. The overall polarization observables of B→ψ(2S)K* 0 and B s→ψ(2S)Φ channels are also in good agreement with the experimental measurements as reported by LHCb and BaBar. In conclusion, other results can also be tested by the LHCb and Belle-II experiments.« less

Color Confinement and Screening in the θ Vacuum of QCD.

PubMed

Kharzeev, Dmitri E; Levin, Eugene M

2015-06-19

QCD perturbation theory ignores the compact nature of the SU(3) gauge group that gives rise to the periodic θ vacuum of the theory. We propose to modify the gluon propagator to reconcile perturbation theory with the anomalous Ward identities for the topological current in the θ vacuum. As a result, the gluon couples to the Veneziano ghost describing the tunneling transitions between different Chern-Simons sectors of the vacuum; we call the emerging gluon dressed by ghost loops a "glost." We evaluate the glost propagator and find that it has the form G(p)=(p(2)+χ(top)/p(2))(-1) where χ(top) is the Yang-Mills topological susceptibility related to the η' mass by the Witten-Veneziano relation; this propagator describes the confinement of gluons at distances ∼χ(top)(-1/4)≃1  fm. The same functional form of the propagator was originally proposed by Gribov as a solution to the gauge copies problem that plagues perturbation theory. The resulting running coupling coincides with the perturbative one at p(2)≫√[χ(top)], but in the infrared region either freezes (in pure Yang-Mills theory) or vanishes (in full QCD with light quarks), in accord with experimental evidence. Our scenario makes explicit the connection between confinement and topology of the QCD vacuum; we discuss the implications for spin physics, high energy scattering, and the physics of quark-gluon plasma.

Solution structure of the C-terminal X domain of the measles virus phosphoprotein and interaction with the intrinsically disordered C-terminal domain of the nucleoprotein.

PubMed

Gely, Stéphane; Lowry, David F; Bernard, Cédric; Jensen, Malene R; Blackledge, Martin; Costanzo, Stéphanie; Bourhis, Jean-Marie; Darbon, Hervé; Daughdrill, Gary; Longhi, Sonia

2010-01-01

In this report, the solution structure of the nucleocapsid-binding domain of the measles virus phosphoprotein (XD, aa 459-507) is described. A dynamic description of the interaction between XD and the disordered C-terminal domain of the nucleocapsid protein, (N(TAIL), aa 401-525), is also presented. XD is an all alpha protein consisting of a three-helix bundle with an up-down-up arrangement of the helices. The solution structure of XD is very similar to the crystal structures of both the free and bound form of XD. One exception is the presence of a highly dynamic loop encompassing XD residues 489-491, which is involved in the embedding of the alpha-helical XD-binding region of N(TAIL). Secondary chemical shift values for full-length N(TAIL) were used to define the precise boundaries of a transient helical segment that coincides with the XD-binding domain, thus shedding light on the pre-recognition state of N(TAIL). Titration experiments with unlabeled XD showed that the transient alpha-helical conformation of N(TAIL) is stabilized upon binding. Lineshape analysis of NMR resonances revealed that residues 483-506 of N(TAIL) are in intermediate exchange with XD, while the 475-482 and 507-525 regions are in fast exchange. The N(TAIL) resonance behavior in the titration experiments is consistent with a complex binding model with more than two states.

Entropic benefit of a cross-link in protein association.

PubMed

Zaman, Muhammad H; Berry, R Stephen; Sosnick, Tobin R

2002-08-01

We introduce a method to estimate the loss of configurational entropy upon insertion of a cross-link to a dimeric system. First, a clear distinction is established between the loss of entropy upon tethering and binding, two quantities that are often considered to be equivalent. By comparing the probability distribution of the center-to-center distances for untethered and cross-linked versions, we are able to calculate the loss of translational entropy upon cross-linking. The distribution function for the untethered helices is calculated from the probability that a given helix is closer to its partner than to all other helices, the "Nearest Neighbor" method. This method requires no assumptions about the nature of the solvent, and hence resolves difficulties normally associated with calculations for systems in liquids. Analysis of the restriction of angular freedom upon tethering indicates that the loss of rotational entropy is negligible. The method is applied in the context of the folding of a ten turn helical coiled coil with the tether modeled as a Gaussian chain or a flexible amino acid chain. After correcting for loop closure entropy in the docked state, we estimate the introduction of a six-residue tether in the coiled coil results in an effective concentration of the chain to be about 4 or 100 mM, depending upon whether the helices are denatured or pre-folded prior to their association. Thus, tethering results in significant stabilization for systems with millimolar or stronger dissociation constants. Copyright 2002 Wiley-Liss, Inc.

The NMR solution structure of a mutant of the Max b/HLH/LZ free of DNA: insights into the specific and reversible DNA binding mechanism of dimeric transcription factors.

PubMed

Sauvé, Simon; Tremblay, Luc; Lavigne, Pierre

2004-09-17

Basic region-helix1-loop-helix2-leucine zipper (b/H(1)LH(2)/LZ) transcription factors bind specific DNA sequence in their target gene promoters as dimers. Max, a b/H(1)LH(2)/LZ transcription factor, is the obligate heterodimeric partner of the related b/H(1)LH(2)/LZ proteins of the Myc and Mad families. These heterodimers specifically bind E-box DNA sequence (CACGTG) to activate (e.g. c-Myc/Max) and repress (e.g. Mad1/Max) transcription. Max can also homodimerize and bind E-box sequences in c-Myc target gene promoters. While the X-ray structure of the Max b/H(1)LH(2)/LZ/DNA complex and that of others have been reported, the precise sequence of events leading to the reversible and specific binding of these important transcription factors is still largely unknown. In order to provide insights into the DNA binding mechanism, we have solved the NMR solution structure of a covalently homodimerized version of a Max b/H(1)LH(2)/LZ protein with two stabilizing mutations in the LZ, and characterized its backbone dynamics from (15)N spin-relaxation measurements in the absence of DNA. Apart from minor differences in the pitch of the LZ, possibly resulting from the mutations in the construct, we observe that the packing of the helices in the H(1)LH(2) domain is almost identical to that of the two crystal structures, indicating that no important conformational change in these helices occurs upon DNA binding. Conversely to the crystal structures of the DNA complexes, the first 14 residues of the basic region are found to be mostly unfolded while the loop is observed to be flexible. This indicates that these domains undergo conformational changes upon DNA binding. On the other hand, we find the last four residues of the basic region form a persistent helical turn contiguous to H(1). In addition, we provide evidence of the existence of internal motions in the backbone of H(1) that are of larger amplitude and longer time-scale (nanoseconds) than the ones in the H(2) and LZ domain. Most interestingly, we note that conformers in the ensemble of calculated structures have highly conserved basic residues (located in the persistent helical turn of the basic region and in the loop) known to be important for specific binding in a conformation that matches that of the DNA-bound state. These partially prefolded conformers can directly fit into the major groove of DNA and as such are proposed to lie on the pathway leading to the reversible and specific DNA binding. In these conformers, the conserved basic side-chains form a cluster that elevates the local electrostatic potential and could provide the necessary driving force for the generation of the internal motions localized in the H(1) and therefore link structural determinants with the DNA binding function. Overall, our results suggests that the Max homodimeric b/H(1)LH(2)/LZ can rapidly and preferentially bind DNA sequence through transient and partially prefolded states and subsequently, adopt the fully helical bound state in a DNA-assisted mechanism or induced-fit.

A small modified hammerhead ribozyme and its conformational characteristics determined by mutagenesis and lattice calculation.

PubMed Central

Lustig, B; Lin, N H; Smith, S M; Jernigan, R L; Jeang, K T

1995-01-01

A prototypic hammerhead ribozyme has three helices that surround an asymmetrical central core loop. We have mutagenized a hammerhead type ribozyme. In agreement with previous studies, progressive removal of stem-loop II from a three stemmed ribozyme showed that this region is not absolutely critical for catalysis. However, complete elimination of stem II and its loop did reduce, but did not eliminate, function. In a stem-loop II-deleted ribozyme, activity was best preserved when a purine, preferably a G, was present at position 10.1. This G contributed to catalysis irregardless of its role as either one part of a canonical pair with a C residue at 11.1 or a lone nucleotide with C (11.1) deleted. Computational methods using lattices generated 87 million three-dimensional chain forms for a stem-loop II-deleted RNA complex that preserved one potential G.C base pair at positions 10.1 and 11.1. This exhaustive set of chain forms included one major class of structures with G(10.1) being spatially proximal to the GUCX cleavage site of the substrate strand. Strong correlations were observed between colinear arrangement of stems I and III, constraints of base-pairing in the central core loop, and one particular placement of G(10.1) relative to the cleavage site. Our calculations of a stem-loop II-deleted ribozyme indicate that without needing to invoke any other constraints, the inherent asymmetry in the lengths of the two loop strands (3 nt in one and 7 nt in the other) that compose the core and flank G10.1-C11.1 stipulated strongly this particular G placement. This suggests that the hammerhead ribozyme maintains an asymmetry in its internal loop for a necessary structure/function reason. Images PMID:7567466

Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix

PubMed Central

Brown, Jessica A.; Bulkley, David; Wang, Jimin; Valenstein, Max L.; Yario, Therese A.; Steitz, Thomas A.; Steitz, Joan A.

2014-01-01

Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a highly-abundant nuclear long noncoding RNA that promotes malignancy. A 3′-stem-loop structure is predicted to confer stability by engaging a downstream A-rich tract in a triple helix, similar to the expression and nuclear retention element (ENE) from the KSHV polyadenylated nuclear RNA. The 3.1-Å resolution crystal structure of the human MALAT1 ENE and A-rich tract reveals a bipartite triple helix containing stacks of five and four U•A-U triples separated by a C+•G-C triplet and C-G doublet, extended by two A-minor interactions. In vivo decay assays indicate that this blunt-ended triple helix, with the 3′ nucleotide in a U•A-U triple, inhibits rapid nuclear RNA decay. Interruption of the triple helix by the C-G doublet induces a “helical reset” that explains why triple-helical stacks longer than six do not occur in nature. PMID:24952594

Strings with a confining core in a quark-gluon plasma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Layek, Biswanath; Mishra, Ananta P.; Srivastava, Ajit M.

2005-04-01

We consider the intersection of N different interfaces interpolating between different Z{sub N} vacua of an SU(N) gauge theory using the Polyakov loop order parameter. Topological arguments show that at such a stringlike junction, the order parameter should vanish, implying that the core of this string (i.e. the junction region of all the interfaces) is in the confining phase. Using the effective potential for the Polyakov loop proposed by Pisarski for QCD, we use numerical minimization technique and estimate the energy per unit length of the core of this string to be about 2.7 GeV/fm at a temperature about twicemore » the critical temperature. For the parameters used, the interface tension is obtained to be about 7 GeV/fm{sup 2}. Lattice simulation of pure gauge theories should be able to investigate properties of these strings. For QCD with quarks, it has been discussed in the literature that this Z{sub N} symmetry may still be meaningful, with quark contributions leading to explicit breaking of this Z{sub N} symmetry. With this interpretation, such quark-gluon plasma strings may play important role in the evolution of the quark-gluon plasma phase and in the dynamics of quark-hadron transition.« less

Crystal structure of Escherichia coli-expressed Haloarcula marismortui bacteriorhodopsin I in the trimeric form.

PubMed

Shevchenko, Vitaly; Gushchin, Ivan; Polovinkin, Vitaly; Round, Ekaterina; Borshchevskiy, Valentin; Utrobin, Petr; Popov, Alexander; Balandin, Taras; Büldt, Georg; Gordeliy, Valentin

2014-01-01

Bacteriorhodopsins are a large family of seven-helical transmembrane proteins that function as light-driven proton pumps. Here, we present the crystal structure of a new member of the family, Haloarcula marismortui bacteriorhodopsin I (HmBRI) D94N mutant, at the resolution of 2.5 Å. While the HmBRI retinal-binding pocket and proton donor site are similar to those of other archaeal proton pumps, its proton release region is extended and contains additional water molecules. The protein's fold is reinforced by three novel inter-helical hydrogen bonds, two of which result from double substitutions relative to Halobacterium salinarum bacteriorhodopsin and other similar proteins. Despite the expression in Escherichia coli and consequent absence of native lipids, the protein assembles as a trimer in crystals. The unique extended loop between the helices D and E of HmBRI makes contacts with the adjacent protomer and appears to stabilize the interface. Many lipidic hydrophobic tail groups are discernible in the membrane region, and their positions are similar to those of archaeal isoprenoid lipids in the crystals of other proton pumps, isolated from native or native-like sources. All these features might explain the HmBRI properties and establish the protein as a novel model for the microbial rhodopsin proton pumping studies.

Structural and mechanistic insights into Mps1 kinase activation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Wei; Yang, Yuting; Gao, Yuefeng

2010-11-05

Mps1 is one of the several essential kinases whose activation is required for robust mitotic spindle checkpoint signalling. The activity of Mps1 is tightly regulated and increases dramatically during mitosis or in response to spindle damage. To understand the molecular mechanism underlying Mps1 regulation, we determined the crystal structure of the kinase domain of Mps1. The 2.7-{angstrom}-resolution crystal structure shows that the Mps1 kinase domain adopts a unique inactive conformation. Intramolecular interactions between the key Glu residue in the {alpha}C helix of the N-terminal lobe and the backbone amides in the catalytic loop lock the kinase in the inactive conformation.more » Autophosphorylation appears to be a priming event for kinase activation. We identified Mps1 autophosphorylation sites in the activation and the P+1 loops. Whereas activation loop autophosphorylation enhances kinase activity, autophosphorylation at the P+1 loop (T686) is associated with the active kinase. Mutation of T686 autophosphorylation site impairs both autophosphorylation and transphosphorylation. Furthermore, we demonstrated that phosphorylation of T676 may be a priming event for phosphorylation at T686. Finally, we identified two critical lysine residues in the loop between helices {alpha}EF and {alpha}F that are essential for substrate recruitment and maintaining high levels of kinase activity. Our studies reveal critical biochemical mechanisms for Mps1 kinase regulation.« less

An analysis of the nucleon spectrum from lattice partially-quenched QCD

DOE Office of Scientific and Technical Information (OSTI.GOV)

W. Armour; Allton, C. R.; Leinweber, Derek B.

2010-09-01

The chiral extrapolation of the nucleon mass, Mn, is investigated using data coming from 2-flavour partially-quenched lattice simulations. The leading one-loop corrections to the nucleon mass are derived for partially-quenched QCD. A large sample of lattice results from the CP-PACS Collaboration is analysed, with explicit corrections for finite lattice spacing artifacts. The extrapolation is studied using finite range regularised chiral perturbation theory. The analysis also provides a quantitative estimate of the leading finite volume corrections. It is found that the discretisation, finite-volume and partial quenching effects can all be very well described in this framework, producing an extrapolated value ofmore » Mn in agreement with experiment. This procedure is also compared with extrapolations based on polynomial forms, where the results are less encouraging.« less

Resolution to the B→πK puzzle

NASA Astrophysics Data System (ADS)

Li, Hsiang-Nan; Mishima, Satoshi; Sanda, A. I.

2005-12-01

We calculate the important next-to-leading-order contributions to the B→πK, ππ decays from the vertex corrections, the quark loops, and the magnetic penguins in the perturbative QCD approach. It is found that the latter two reduce the leading-order penguin amplitudes by about 10% and modify only the B→πK branching ratios. The main effect of the vertex corrections is to increase the small color-suppressed tree amplitude by a factor of 3, which then resolves the large difference between the direct CP asymmetries of the B0→π∓K± and B±→π0K± modes. The puzzle from the large B0→π0π0 branching ratio still remains.

Predicting RNA folding thermodynamics with a reduced chain representation model

PubMed Central

CAO, SONG; CHEN, SHI-JIE

2005-01-01

Based on the virtual bond representation for the nucleotide backbone, we develop a reduced conformational model for RNA. We use the experimentally measured atomic coordinates to model the helices and use the self-avoiding walks in a diamond lattice to model the loop conformations. The atomic coordinates of the helices and the lattice representation for the loops are matched at the loop–helix junction, where steric viability is accounted for. Unlike the previous simplified lattice-based models, the present virtual bond model can account for the atomic details of realistic three-dimensional RNA structures. Based on the model, we develop a statistical mechanical theory for RNA folding energy landscapes and folding thermodynamics. Tests against experiments show that the theory can give much more improved predictions for the native structures, the thermal denaturation curves, and the equilibrium folding/unfolding pathways than the previous models. The application of the model to the P5abc region of Tetrahymena group I ribozyme reveals the misfolded intermediates as well as the native-like intermediates in the equilibrium folding process. Moreover, based on the free energy landscape analysis for each and every loop mutation, the model predicts five lethal mutations that can completely alter the free energy landscape and the folding stability of the molecule. PMID:16251382

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rothstein, Ira Z.; Stewart, Iain W.

Starting with QCD, we derive an effective field theory description for forward scattering and factorization violation as part of the soft-collinear effective field theory (SCET) for high energy scattering. These phenomena are mediated by long distance Glauber gluon exchanges, which are static in time, localized in the longitudinal distance, and act as a kernel for forward scattering where |t| << s. In hard scattering, Glauber gluons can induce corrections which invalidate factorization. With SCET, Glauber exchange graphs can be calculated explicitly, and are distinct from graphs involving soft, collinear, or ultrasoft gluons. We derive a complete basis of operators whichmore » describe the leading power effects of Glauber exchange. Key ingredients include regulating light-cone rapidity singularities and subtractions which prevent double counting. Our results include a novel all orders gauge invariant pure glue soft operator which appears between two collinear rapidity sectors. The 1-gluon Feynman rule for the soft operator coincides with the Lipatov vertex, but it also contributes to emissions with ≥ 2 soft gluons. Our Glauber operator basis is derived using tree level and one-loop matching calculations from full QCD to both SCET II and SCET I. The one-loop amplitude’s rapidity renormalization involves mixing of color octet operators and yields gluon Reggeization at the amplitude level. The rapidity renormalization group equation for the leading soft and collinear functions in the forward scattering cross section are each given by the BFKL equation. Various properties of Glauber gluon exchange in the context of both forward scattering and hard scattering factorization are described. For example, we derive an explicit rule for when eikonalization is valid, and provide a direct connection to the picture of multiple Wilson lines crossing a shockwave. In hard scattering operators Glauber subtractions for soft and collinear loop diagrams ensure that we are not sensitive to the directions for soft and collinear Wilson lines. Conversely, certain Glauber interactions can be absorbed into these soft and collinear Wilson lines by taking them to be in specific directions. Finally, we also discuss criteria for factorization violation.« less

An effective field theory for forward scattering and factorization violation

DOE PAGES

Rothstein, Ira Z.; Stewart, Iain W.

2016-08-03

Starting with QCD, we derive an effective field theory description for forward scattering and factorization violation as part of the soft-collinear effective field theory (SCET) for high energy scattering. These phenomena are mediated by long distance Glauber gluon exchanges, which are static in time, localized in the longitudinal distance, and act as a kernel for forward scattering where |t| << s. In hard scattering, Glauber gluons can induce corrections which invalidate factorization. With SCET, Glauber exchange graphs can be calculated explicitly, and are distinct from graphs involving soft, collinear, or ultrasoft gluons. We derive a complete basis of operators whichmore » describe the leading power effects of Glauber exchange. Key ingredients include regulating light-cone rapidity singularities and subtractions which prevent double counting. Our results include a novel all orders gauge invariant pure glue soft operator which appears between two collinear rapidity sectors. The 1-gluon Feynman rule for the soft operator coincides with the Lipatov vertex, but it also contributes to emissions with ≥ 2 soft gluons. Our Glauber operator basis is derived using tree level and one-loop matching calculations from full QCD to both SCET II and SCET I. The one-loop amplitude’s rapidity renormalization involves mixing of color octet operators and yields gluon Reggeization at the amplitude level. The rapidity renormalization group equation for the leading soft and collinear functions in the forward scattering cross section are each given by the BFKL equation. Various properties of Glauber gluon exchange in the context of both forward scattering and hard scattering factorization are described. For example, we derive an explicit rule for when eikonalization is valid, and provide a direct connection to the picture of multiple Wilson lines crossing a shockwave. In hard scattering operators Glauber subtractions for soft and collinear loop diagrams ensure that we are not sensitive to the directions for soft and collinear Wilson lines. Conversely, certain Glauber interactions can be absorbed into these soft and collinear Wilson lines by taking them to be in specific directions. Finally, we also discuss criteria for factorization violation.« less

Screech tones from free and ducted supersonic jets

NASA Technical Reports Server (NTRS)

Tam, C. K. W.; Ahuja, K. K.; Jones, R. R., III

1994-01-01

It is well known that screech tones from supersonic jets are generated by a feedback loop. The loop consists of three main components. They are the downstream propagating instability wave, the shock cell structure in the jet plume, and the feedback acoustic waves immediately outside the jet. Evidence will be presented to show that the screech frequency is largely controlled by the characteristics of the feedback acoustic waves. The feedback loop is driven by the instability wave of the jet. Thus the tone intensity and its occurrence are dictated by the characteristics of the instability wave. In this paper the dependence of the instability wave spectrum on the azimuthal mode number (axisymmetric or helical/flapping mode, etc.), the jet-to-ambient gas temperature ratio, and the jet Mach number are studied. The results of this study provide an explanation for the observed screech tone mode switch phenomenon (changing from axisymmetric to helical mode as Mach number increases) and the often-cited experimental observation that tone intensity reduces with increase in jet temperature. For ducted supersonic jets screech tones can also be generated by feedback loops formed by the coupling of normal duct modes to instability waves of the jet. The screech frequencies are dictated by the frequencies of the duct modes. Super resonance, resonance involving very large pressure oscillations, can occur when the feedback loop is powered by the most amplified instability wave. It is proposed that the observed large amplitude pressure fluctuations and tone in the test cells of Arnold Engineering Development Center were generated by super resonance. Estimated super-resonance frequency for a Mach 1.3 axisymmetric jet tested in the facility agrees well with measurement.

PREFACE: Focus section on Hadronic Physics

NASA Astrophysics Data System (ADS)

Roberts, Craig; Swanson, Eric

2007-07-01

Hadronic physics is the study of strongly interacting matter and its underlying theory, Quantum Chromodynamics (QCD). The field had its beginnings after World War Two, when hadrons were discovered in ever increasing numbers. Today, it encompasses topics like the quark-gluon structure of hadrons at varying scales, the quark-gluon plasma and hadronic matter at extreme temperature and density; it also underpins nuclear physics and has significant impact on particle physics, astrophysics, and cosmology. Among the goals of hadronic physics are to determine the parameters of QCD, understand the origin and characteristics of confinement, understand the dynamics and consequences of dynamical chiral symmetry breaking, explore the role of quarks and gluons in nuclei and in matter under extreme conditions and understand the quark and gluon structure of hadrons. In general, the process is one of discerning the relevant degrees of freedom and relating these to the fundamental fields of QCD. The emphasis is on understanding QCD, rather than testing it. The papers gathered in this special focus section of Journal of Physics G: Nuclear and Particle Physics attempt to cover this broad range of subjects. Alkofer and Greensite examine the issue of quark and gluon confinement with the focus on models of the QCD vacuum, lattice gauge theory investigations, and the relationship to the AdS/CFT correspondence postulate. Arrington et al. review nucleon form factors and their role in determining quark orbital momentum, the strangeness content of the nucleon, meson cloud effects, and the transition from nonperturbative to perturbative QCD dynamics. The physics associated with hadronic matter at high temperature and density and at low Bjorken-x at the Relativistic Heavy Ion Collider (RHIC), the SPS at CERN, and at the future LHC is summarized by d'Enterria. The article of Lee and Smith examines experiment and theory associated with electromagnetic meson production from nucleons and illustrates how the structure of the nucleon is revealed. Reimer reviews how the Drell--Yan process can be used to explore the sea quark structure of nucleons, thereby probing such phenomena as flavour asymmetry in the nucleon and nuclear medium modification of nucleon properties. The exploitation of the B factories has led to a resurgence of interest in heavy quark spectroscopy. Concurrently, interest in light quark spectroscopy and gluonic excitations remains high, with several new experimental efforts in the planning or building stages. The current status of all of this is reviewed by Rosner. Finally, Vogelsang summarizes the status of polarized deep inelastic lepton-nucleon scattering experiments at RHIC and their impact on the theoretical understanding of nucleon helicity structure, gluon polarization in the nucleus, and transverse spin asymmetries. Of course, hadronic physics is a much broader subject than can be conveyed in this special focus section; advances in effective field theory, lattice gauge theory, generalised parton distributions and many other subfields are not covered here. Nevertheless, we hope that this focus section will help the reader appreciate the vitality, breadth of endeavour, and the phenomenological richness of hadronic physics.

Advancing High Current Startup via Localized Helicity Injection in the PEGASUS Toroidal Experiment

NASA Astrophysics Data System (ADS)

Hinson, E. T.; Barr, J. L.; Bongard, M. W.; Burke, M. G.; Fonck, R. J.; Perry, J. M.; Redd, A. J.; Schlossberg, D. J.

2013-10-01

Non-solenoidal startup via local helicity injection (LHI) and poloidal field induction is used to produce Ip = 0 . 17 MA tokamak discharges. Impurity contamination has been reduced to negligible levels by use of conical frustum cathode geometry and local scraper limiters. Attainable currents are governed by global limits of helicity and energy balance, and Taylor relaxation. A simple lumped parameter model based on these limits is used to project discharge evolution, and indicates that attaining 1 MA in NSTX-U will require LHI-driven effective loop voltages to dominate contributions from dLp / dt . This regime contrasts with results to date and will be tested at 0.3 MA in PEGASUS with a new integrated multi-injector array. Injector impedance characteristics are consistent with magnetically-limited regimes observed in higher-power foilless diodes. Bursts of MHD are measured on time scales of order ~ 100 μ s, and correlate with rapid equilibrium changes, discrete rises in Ip, redistribution of the toroidal current, ion heating (Ti ~ 1 keV), transient drops in injector voltage, and apparent n = 1 line-tied kink activity at the injector. NIMROD simulations of high-field-side HI discharges in PEGASUS are in qualitative agreement, suggesting Ip buildup results from inward propagating toroidal current loops created by intermittent reconnection of injected current streams. Work supported by US DOE Grant DE-FG02-96ER54375.

Renormalization of quark bilinear operators in a momentum-subtraction scheme with a nonexceptional subtraction point

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sturm, C.; Soni, A.; Aoki, Y.

2009-07-01

We extend the Rome-Southampton regularization independent momentum-subtraction renormalization scheme (RI/MOM) for bilinear operators to one with a nonexceptional, symmetric subtraction point. Two-point Green's functions with the insertion of quark bilinear operators are computed with scalar, pseudoscalar, vector, axial-vector and tensor operators at one-loop order in perturbative QCD. We call this new scheme RI/SMOM, where the S stands for 'symmetric'. Conversion factors are derived, which connect the RI/SMOM scheme and the MS scheme and can be used to convert results obtained in lattice calculations into the MS scheme. Such a symmetric subtraction point involves nonexceptional momenta implying a lattice calculation withmore » substantially suppressed contamination from infrared effects. Further, we find that the size of the one-loop corrections for these infrared improved kinematics is substantially decreased in the case of the pseudoscalar and scalar operator, suggesting a much better behaved perturbative series. Therefore it should allow us to reduce the error in the determination of the quark mass appreciably.« less

Two-baryon systems from HAL QCD method and the mirage in the temporal correlation of the direct method

NASA Astrophysics Data System (ADS)

Iritani, Takumi

2018-03-01

Both direct and HAL QCD methods are currently used to study the hadron interactions in lattice QCD. In the direct method, the eigen-energy of two-particle is measured from the temporal correlation. Due to the contamination of excited states, however, the direct method suffers from the fake eigen-energy problem, which we call the "mirage problem," while the HAL QCD method can extract information from all elastic states by using the spatial correlation. In this work, we further investigate systematic uncertainties of the HAL QCD method such as the quark source operator dependence, the convergence of the derivative expansion of the non-local interaction kernel, and the single baryon saturation, which are found to be well controlled. We also confirm the consistency between the HAL QCD method and the Lüscher's finite volume formula. Based on the HAL QCD potential, we quantitatively confirm that the mirage plateau in the direct method is indeed caused by the contamination of excited states.

NMR structure and localization of a large fragment of the SARS-CoV fusion protein: Implications in viral cell fusion.

PubMed

Mahajan, Mukesh; Chatterjee, Deepak; Bhuvaneswari, Kannaian; Pillay, Shubhadra; Bhattacharjya, Surajit

2018-02-01

The lethal Coronaviruses (CoVs), Severe Acute Respiratory Syndrome-associated Coronavirus (SARS-CoV) and most recently Middle East Respiratory Syndrome Coronavirus, (MERS-CoV) are serious human health hazard. A successful viral infection requires fusion between virus and host cells carried out by the surface spike glycoprotein or S protein of CoV. Current models propose that the S2 subunit of S protein assembled into a hexameric helical bundle exposing hydrophobic fusogenic peptides or fusion peptides (FPs) for membrane insertion. The N-terminus of S2 subunit of SARS-CoV reported to be active in cell fusion whereby FPs have been identified. Atomic-resolution structure of FPs derived either in model membranes or in membrane mimic environment would glean insights toward viral cell fusion mechanism. Here, we have solved 3D structure, dynamics and micelle localization of a 64-residue long fusion peptide or LFP in DPC detergent micelles by NMR methods. Micelle bound structure of LFP is elucidated by the presence of discretely folded helical and intervening loops. The C-terminus region, residues F42-Y62, displays a long hydrophobic helix, whereas the N-terminus is defined by a short amphipathic helix, residues R4-Q12. The intervening residues of LFP assume stretches of loops and helical turns. The N-terminal helix is sustained by close aromatic and aliphatic sidechain packing interactions at the non-polar face. 15 N{ 1 H}NOE studies indicated dynamical motion, at ps-ns timescale, of the helices of LFP in DPC micelles. PRE NMR showed that insertion of several regions of LFP into DPC micelle core. Together, the current study provides insights toward fusion mechanism of SARS-CoV. Copyright © 2017 Elsevier B.V. All rights reserved.

The Tip of the Four N-Terminal α-Helices of Clostridium sordellii Lethal Toxin Contains the Interaction Site with Membrane Phosphatidylserine Facilitating Small GTPases Glucosylation

PubMed Central

Varela Chavez, Carolina; Haustant, Georges Michel; Baron, Bruno; England, Patrick; Chenal, Alexandre; Pauillac, Serge; Blondel, Arnaud; Popoff, Michel-Robert

2016-01-01

Clostridium sordellii lethal toxin (TcsL) is a powerful virulence factor responsible for severe toxic shock in man and animals. TcsL belongs to the large clostridial glucosylating toxin (LCGT) family which inactivates small GTPases by glucosylation with uridine-diphosphate (UDP)-glucose as a cofactor. Notably, TcsL modifies Rac and Ras GTPases, leading to drastic alteration of the actin cytoskeleton and cell viability. TcsL enters cells via receptor-mediated endocytosis and delivers the N-terminal glucosylating domain (TcsL-cat) into the cytosol. TcsL-cat was found to preferentially bind to phosphatidylserine (PS)-containing membranes and to increase the glucosylation of Rac anchored to the lipid membrane. We have previously reported that the N-terminal four helical bundle structure (1–93 domain) recognizes a broad range of lipids, but that TcsL-cat specifically binds to PS and phosphatidic acid. Here, we show using mutagenesis that the PS binding site is localized on the tip of the four-helix bundle which is rich in positively-charged amino acids. Residues Y14, V15, F17, and R18 on loop 1, between helices 1 and 2, in coordination with R68 from loop 3, between helices 3 and 4, form a pocket which accommodates L-serine. The functional PS-binding site is required for TcsL-cat binding to the plasma membrane and subsequent cytotoxicity. TcsL-cat binding to PS facilitates a high enzymatic activity towards membrane-anchored Ras by about three orders of magnitude as compared to Ras in solution. The PS-binding site is conserved in LCGTs, which likely retain a common mechanism of binding to the membrane for their full activity towards membrane-bound GTPases. PMID:27023605

Hadronic light-by-light scattering contribution to the muon anomalous magnetic moment from lattice QCD.

PubMed

Blum, Thomas; Chowdhury, Saumitra; Hayakawa, Masashi; Izubuchi, Taku

2015-01-09

The most compelling possibility for a new law of nature beyond the four fundamental forces comprising the standard model of high-energy physics is the discrepancy between measurements and calculations of the muon anomalous magnetic moment. Until now a key part of the calculation, the hadronic light-by-light contribution, has only been accessible from models of QCD, the quantum description of the strong force, whose accuracy at the required level may be questioned. A first principles calculation with systematically improvable errors is needed, along with the upcoming experiments, to decisively settle the matter. For the first time, the form factor that yields the light-by-light scattering contribution to the muon anomalous magnetic moment is computed in such a framework, lattice QCD+QED and QED. A nonperturbative treatment of QED is used and checked against perturbation theory. The hadronic contribution is calculated for unphysical quark and muon masses, and only the diagram with a single quark loop is computed for which statistically significant signals are obtained. Initial results are promising, and the prospect for a complete calculation with physical masses and controlled errors is discussed.

Quadrifilar Helical Antenna Array for Line-of-Sight Communications Above the Ocean Surface

DTIC Science & Technology

2007-06-25

placing the copper-covered sheet into a mechanical plotter and using a diamond scribe to cut the edges. 5 27 (a) i (bI 900 PUTTR 180 SPTTER ANTENN 11Z...soldering of the cable to the hole and to avoid any possible radio frequency (RF) ground loops that may form. However, because it was determined that...prevent any RF ground loops that may be produced that could induce undesirable currents along the brass tube. Figure 4-9 is a closeup view of an

Fluorescence spectroscopic characterization of Humicola lanuginosa lipase dissolved in its substrate.

PubMed

Jutila, Arimatti; Zhu, Keng; Tuominen, Esa K J; Kinnunen, Paavo K J

2004-11-01

The conformational dynamics of Humicola lanuginosa lipases (HLL) and its three mutants were investigated by steady state and time-resolved fluorescence spectroscopy in two different media, aqueous buffer and the substrate triacetin. The fluorescence of the four Trps of the wild-type HLL (wt) reports on the global changes of the whole lipase molecule. In order to monitor conformational changes specifically in the alpha-helical surface loop, the so-called 'lid' of HLL comprised of residues 86-93, the single Trp mutant W89m (W117F, W221H, W260H) was employed. Mutants W89L and W89mN33Q (W117F, W221H, W260H, N33Q) were used to survey the impact of Trp89 and mannose residues, respectively. Based on the data obtained, the following conclusions can be drawn. (i) HLL adapts the 'open' conformation in triacetin, with the alpha-helical surface loop moving so as to expose the active site. (ii) Trp89 contained in the lid plays an unprecedently important role in the structural stability of HLL. (iii) In triacetin, but not in the buffer, the motion of the Trp89 side chain becomes distinguishable from the motion of the lid. (iv) The carbohydrate moiety at Asn33 has only minor effects on the dynamics of Trp89 in the lid as judged from the fluorescence characteristics of the latter residue.

The 1.25 Å resolution structure of phosphoribosyl-ATP pyrophosphohydrolase from Mycobacterium tuberculosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Javid-Majd, Farah; Yang, Dong; Ioerger, Thomas R.

2008-06-23

Phosphoribosyl-ATP pyrophosphohydrolase is the second enzyme in the histidine-biosynthetic pathway, irreversibly hydrolyzing phosphoribosyl-ATP to phosphoribosyl-AMP and pyrophosphate. It is encoded by the hisE gene, which is present as a separate gene in many bacteria and archaea but is fused to hisI in other bacteria, fungi and plants. Because of its essentiality for growth in vitro, HisE is a potential drug target for tuberculosis. The crystal structures of two native (uncomplexed) forms of HisE from Mycobacterium tuberculosis have been determined to resolutions of 1.25 and 1.79 {angstrom}. The structure of the apoenzyme reveals that the protein is composed of five -helicesmore » with connecting loops and is a member of the {alpha}-helical nucleoside-triphosphate pyrophosphatase superfamily. The biological unit of the protein is a homodimer, with an active site on each subunit composed of residues exclusively from that subunit. A comparison with the Campylobacter jejuni dUTPase active site allowed the identification of putative metal- and substrate-binding sites in HisE, including four conserved glutamate and glutamine residues in the sequence that are consistent with a motif for pyrophosphohydrolase activity. However, significant differences between family members are observed in the loop region between {alpha}-helices H1 and H3. The crystal structure of M. tuberculosis HisE provides insights into possible mechanisms of substrate binding and the diversity of the nucleoside-triphosphate pyrophosphatase superfamily.« less

HELAC-Onia 2.0: An upgraded matrix-element and event generator for heavy quarkonium physics

NASA Astrophysics Data System (ADS)

Shao, Hua-Sheng

2016-01-01

We present an upgraded version (denoted as version 2.0) of the program HELAC-ONIA for the automated computation of heavy-quarkonium helicity amplitudes within non-relativistic QCD framework. The new code has been designed to include many new and useful features for practical phenomenological simulations. It is designed for job submissions under cluster environment for parallel computations via PYTHON scripts. We have interfaced HELAC-ONIA to the parton shower Monte Carlo programs PYTHIA 8 and QEDPS to take into account the parton-shower effects. Moreover, the decay module guarantees that the program can perform the spin-entangled (cascade-)decay of heavy quarkonium after its generation. We have also implemented a reweighting method to automatically estimate the uncertainties from renormalization and/or factorization scales as well as parton-distribution functions to weighted or unweighted events. A further update is the possibility to generate one-dimensional or two-dimensional plots encoded in the analysis files on the fly. Some dedicated examples are given at the end of the writeup.

The Theory of High Energy Collision Processes - Final Report DOE/ER/40158-1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Tai, T.

In 1984, DOE awarded Harvard University a new Grant DE-FG02-84ER40158 to continue their support of Tai Tsun Wu as Principal Investigator of research on the theory of high energy collision processes. This Grant was renewed and remained active continuously from June 1, 1984 through November 30, 2007. Topics of interest during the 23-year duration of this Grant include: the theory and phenomenology of collision and production processes at ever higher energies; helicity methods of QED and QCD; neutrino oscillations and masses; Yang-Mills gauge theory; Beamstrahlung; Fermi pseudopotentials; magnetic monopoles and dyons; cosmology; classical confinement; mass relations; Bose-Einstein condensation; and large-momentum-transfermore » scattering processes. This Final Report describes the research carried out on Grant DE-FG02-84ER40158 for the period June 1, 1984 through November 30, 2007. Two books resulted from this project and a total of 125 publications.« less

Chiral perturbation theory and nucleon-pion-state contaminations in lattice QCD

NASA Astrophysics Data System (ADS)

Bär, Oliver

2017-05-01

Multiparticle states with additional pions are expected to be a non-negligible source of excited-state contamination in lattice simulations at the physical point. It is shown that baryon chiral perturbation theory can be employed to calculate the contamination due to two-particle nucleon-pion-states in various nucleon observables. Leading order results are presented for the nucleon axial, tensor and scalar charge and three Mellin moments of parton distribution functions (quark momentum fraction, helicity and transversity moment). Taking into account phenomenological results for the charges and moments the impact of the nucleon-pion-states on lattice estimates for these observables can be estimated. The nucleon-pion-state contribution results in an overestimation of all charges and moments obtained with the plateau method. The overestimation is at the 5-10% level for source-sink separations of about 2 fm. The source-sink separations accessible in contemporary lattice simulations are found to be too small for chiral perturbation theory to be directly applicable.

Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures

PubMed Central

Sloma, Michael F.; Mathews, David H.

2016-01-01

RNA secondary structure prediction is widely used to analyze RNA sequences. In an RNA partition function calculation, free energy nearest neighbor parameters are used in a dynamic programming algorithm to estimate statistical properties of the secondary structure ensemble. Previously, partition functions have largely been used to estimate the probability that a given pair of nucleotides form a base pair, the conditional stacking probability, the accessibility to binding of a continuous stretch of nucleotides, or a representative sample of RNA structures. Here it is demonstrated that an RNA partition function can also be used to calculate the exact probability of formation of hairpin loops, internal loops, bulge loops, or multibranch loops at a given position. This calculation can also be used to estimate the probability of formation of specific helices. Benchmarking on a set of RNA sequences with known secondary structures indicated that loops that were calculated to be more probable were more likely to be present in the known structure than less probable loops. Furthermore, highly probable loops are more likely to be in the known structure than the set of loops predicted in the lowest free energy structures. PMID:27852924

Baryon currents in QCD with compact dimensions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lucini, B.; Patella, A.; Istituto Nazionale Fisica Nucleare Sezione di Pisa, Largo Pontecorvo 3, 56126 Pisa

2007-06-15

On a compact space with nontrivial cycles, for sufficiently small values of the radii of the compact dimensions, SU(N) gauge theories coupled with fermions in the fundamental representation spontaneously break charge conjugation, time reversal, and parity. We show at one loop in perturbation theory that a physical signature for this phenomenon is a nonzero baryonic current wrapping around the compact directions. The persistence of this current beyond the perturbative regime is checked by lattice simulations.

Aspects of baryon structure in lattice QCD

NASA Astrophysics Data System (ADS)

Babich, Ronald

Despite the long success of Quantum Chromodynamics (QCD) as the theory of the strong interactions, there remains much to be understood about the structure of hadrons and the consequences of QCD in the nonperturbative regime. Lattice gauge theory, a framework nearly as old as QCD itself, makes calculations in this regime possible, starting from first principles. With advances in theoretical understanding, methods, and computer technology, the lattice has found application to an ever-widening range of problems. In this dissertation, I consider two such problems having to do with the structure of baryons. The first concerns the contribution of sea quarks, and the strange quark in particular, to form factors of the nucleon. This has been a long-standing challenge for the lattice, because such contributions involve the insertion of a current on a quark loop, demanding the full inversion of the discretized Dirac operator, conceptually a large sparse matrix. I discuss methods for addressing this challenge and present a calculation of the strange scalar form factor and the related parameter fTs. The latter is of great theoretical interest, since it enters into the cross section for the scattering of dark matter off nuclei in supersymmetric extensions of the standard model. As such, it represents a major uncertainty in the interpretation of direct detection experiments. I also present results for the strange quark contribution to the nucleon's axial and electromagnetic form factors, which are themselves the subject of active experimental programs. These calculations were performed using the Wilson fermion formulation on a 243 x 64 anisotropic lattice. In the second part of the dissertation, I turn to the valence sector and address the role of diquark correlations in the observed spectrum of hadrons and their properties. A diquark is a correlated pair of quarks, thought to play an important role in certain phenomenological models of hadrons. I present results for baryon wave functions, evaluated in both the Coulomb and Landau gauges. By comparing baryons that differ in their diquark content, I find evidence for enhanced correlation in the scalar diquark channel, as favored by QCD-inspired quark models. I also present results for diquark mass splittings, determined from diquark correlators in the Landau gauge. This second set of calculations was performed with the overlap Dirac operator on quenched gauge configurations at beta = 6.

Scalar production and decay to top quarks including interference effects at NLO in QCD in an EFT approach

DOE PAGES

Franzosi, Diogo Buarque; Vryonidou, Eleni; Zhang, Cen

2017-10-13

Scalar and pseudo-scalar resonances decaying to top quarks are common predictions in several scenarios beyond the standard model (SM) and are extensively searched for by LHC experiments. Challenges on the experimental side require optimising the strategy based on accurate predictions. Firstly, QCD corrections are known to be large both for the SM QCD background and for the pure signal scalar production. Secondly, leading order and approximate next-to-leading order (NLO) calculations indicate that the interference between signal and background is large and drastically changes the lineshape of the signal, from a simple peak to a peak-dip structure. Therefore, a robust predictionmore » of this interference at NLO accuracy in QCD is necessary to ensure that higher-order corrections do not alter the lineshapes. We compute the exact NLO corrections, assuming a point-like coupling between the scalar and the gluons and consistently embedding the calculation in an effective field theory within an automated framework, and present results for a representative set of beyond the SM benchmarks. The results can be further matched to parton shower simulation, providing more realistic predictions. We find that NLO corrections are important and lead to a significant reduction of the uncertainties. We also discuss how our computation can be used to improve the predictions for physics scenarios where the gluon-scalar loop is resolved and the effective approach is less applicable.« less

Color Confinement and Screening in the θ Vacuum of QCD

DOE PAGES

Kharzeev, Dmitri E.; Levin, Eugene M.

2015-06-16

QCD perturbation theory ignores the compact nature of the SU(3) gauge group that gives rise to the periodic θ vacuum of the theory. In this paper, we propose to modify the gluon propagator to reconcile perturbation theory with the anomalous Ward identities for the topological current in the θ vacuum. As a result, the gluon couples to the Veneziano ghost describing the tunneling transitions between different Chern-Simons sectors of the vacuum; we call the emerging gluon dressed by ghost loops a “glost.” We evaluate the glost propagator and find that it has the form G(p)=(p 2+χ top/p 2) -1 wheremore » χ top is the Yang-Mills topological susceptibility related to the η" mass by the Witten-Veneziano relation; this propagator describes the confinement of gluons at distances ~χ top -1/4≃1 fm. The same functional form of the propagator was originally proposed by Gribov as a solution to the gauge copies problem that plagues perturbation theory. The resulting running coupling coincides with the perturbative one at p 2>>√χtop, but in the infrared region either freezes (in pure Yang-Mills theory) or vanishes (in full QCD with light quarks), in accord with experimental evidence. In conclusion, our scenario makes explicit the connection between confinement and topology of the QCD vacuum; we discuss the implications for spin physics, high energy scattering, and the physics of quark-gluon plasma.« less

Scalar production and decay to top quarks including interference effects at NLO in QCD in an EFT approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Franzosi, Diogo Buarque; Vryonidou, Eleni; Zhang, Cen

Scalar and pseudo-scalar resonances decaying to top quarks are common predictions in several scenarios beyond the standard model (SM) and are extensively searched for by LHC experiments. Challenges on the experimental side require optimising the strategy based on accurate predictions. Firstly, QCD corrections are known to be large both for the SM QCD background and for the pure signal scalar production. Secondly, leading order and approximate next-to-leading order (NLO) calculations indicate that the interference between signal and background is large and drastically changes the lineshape of the signal, from a simple peak to a peak-dip structure. Therefore, a robust predictionmore » of this interference at NLO accuracy in QCD is necessary to ensure that higher-order corrections do not alter the lineshapes. We compute the exact NLO corrections, assuming a point-like coupling between the scalar and the gluons and consistently embedding the calculation in an effective field theory within an automated framework, and present results for a representative set of beyond the SM benchmarks. The results can be further matched to parton shower simulation, providing more realistic predictions. We find that NLO corrections are important and lead to a significant reduction of the uncertainties. We also discuss how our computation can be used to improve the predictions for physics scenarios where the gluon-scalar loop is resolved and the effective approach is less applicable.« less

Continuous Advances in QCD 2008

NASA Astrophysics Data System (ADS)

Peloso, Marco M.

2008-12-01

1. High-order calculations in QCD and in general gauge theories. NLO evolution of color dipoles / I. Balitsky. Recent perturbative results on heavy quark decays / J. H. Piclum, M. Dowling, A. Pak. Leading and non-leading singularities in gauge theory hard scattering / G. Sterman. The space-cone gauge, Lorentz invariance and on-shell recursion for one-loop Yang-Mills amplitudes / D. Vaman, Y.-P. Yao -- 2. Heavy flavor physics. Exotic cc¯ mesons / E. Braaten. Search for new physics in B[symbol]-mixing / A. J. Lenz. Implications of D[symbol]-D[symbol] mixing for new physics / A. A. Petrov. Precise determinations of the charm quark mass / M. Steinhauser -- 3. Quark-gluon dynamics at high density and/or high temperature. Crystalline condensate in the chiral Gross-Neveu model / G. V. Dunne, G. Basar. The strong coupling constant at low and high energies / J. H. Kühn. Quarkyonic matter and the phase diagram of QCD / L. McLerran. Statistical QCD with non-positive measure / J. C. Osborn, K. Splittorff, J. J. M. Verbaarschot. From equilibrium to transport properties of strongly correlated fermi liquids / T. Schäfer. Lessons from random matrix theory for QCD at finite density / K. Splittorff, J. J. M. Verbaarschot -- 4. Methods and models of holographic correspondence. Soft-wall dynamics in AdS/QCD / B. Batell. Holographic QCD / N. Evans, E. Threlfall. QCD glueball sum rules and vacuum topology / H. Forkel. The pion form factor in AdS/QCD / H. J. Kwee, R. F. Lebed. The fast life of holographic mesons / R. C. Myers, A. Sinha. Properties of Baryons from D-branes and instantons / S. Sugimoto. The master space of N = 1 quiver gauge theories: counting BPS operators / A. Zaffaroni. Topological field congurations. Skyrmions in theories with massless adjoint quarks / R. Auzzi. Domain walls, localization and confinement: what binds strings inside walls / S. Bolognesi. Static interactions of non-abelian vortices / M. Eto. Vortices which do not abelianize dynamically: semi-classical origin of non-abelian monopoles / K. Konishi. A generalized construction for lumps and non-abelian vortices / W. Vinci -- 6. Dynamics in supersymmetric theories. Cusp anomalous dimension in planar maximally supersymmetric Yang-Mills theory / B. Basso. SO(2M) and USp(2M) (hyper)Kähler quotients and lumps / S. B. Gudnason -- 7. Other developments. Gluinos condensing at the CCNI: 4096 CPUs weigh in / J. Giedt ... [et al.]. Baryon Regge trajectories and the 1/N[symbol] expansion / J. L. Goity, N. Matagne. Infrared behavior of the fermion propagator in unquenched QED[symbol] with finite threshold effects / Y. Hoshino. Gauge fields in accelerated frames / F. Lenz. QCD at complex coupling, large order in perturbation theory and the gluon condensate / Y. Meurice. 511 KeV line and other diffuse emissions as a trace of the dark matter / A. R. Zhitnitsky -- 8. Glimpses of the conference.

Electroexcitation of nucleon resonances from CLAS data on single pion electroproduction

DOE Office of Scientific and Technical Information (OSTI.GOV)

I. G. Aznauryan, V. D. Burkert

2009-11-01

We present results on the electroexcitation of the low mass resonances Delta(1232)P33, N(1440)P11, N(1520)D13, and N(1535)S11 in a wide range of Q2. The results were obtained in the comprehensive analysis of JLab-CLAS data on differential cross sections, longitudinally polarized beam asymmetries, and longitudinal target and beam-target asymmetries for pion electroproduction off the proton. The data were analysed using two conceptually different approaches, fixed-t dispersion relations and a unitary isobar model, allowing us to draw conclusions on the model sensitivity of the obtained electrocoupling amplitudes. The amplitudes for the Delta(1232)P33} show the importance of a meson-cloud contribution to quantitatively explain themore » magnetic dipole strength, as well as the electric and scalar quadrupole transitions. They do not show any tendency of approaching the pQCD regime for Q2<6 GeV2. For the Roper resonance, N(1440)P11, the data provide strong evidence for this state as a predominantly radial excitation of a 3-quark ground state. Measured in pion electroproduction, the transverse helicity amplitude for the N(1535)S11 allowed us to obtain the branching ratios of this state to the piN and etaN channels via comparison to the results extracted from eta electroproduction. The extensive CLAS data also enabled the extraction of the gamma*p -> N(1520)D13 and N(1535)S11 longitudinal helicity amplitudes with good precision.« less

Relations between heavy-light meson and quark masses

NASA Astrophysics Data System (ADS)

Brambilla, N.; Komijani, J.; Kronfeld, A. S.; Vairo, A.; Tumqcd Collaboration

2018-02-01

The study of heavy-light meson masses should provide a way to determine renormalized quark masses and other properties of heavy-light mesons. In the context of lattice QCD, for example, it is possible to calculate hadronic quantities for arbitrary values of the quark masses. In this paper, we address two aspects relating heavy-light meson masses to the quark masses. First, we introduce a definition of the renormalized quark mass that is free of both scale dependence and renormalon ambiguities, and discuss its relation to more familiar definitions of the quark mass. We then show how this definition enters a merger of the descriptions of heavy-light masses in heavy-quark effective theory and in chiral perturbation theory (χ PT ). For practical implementations of this merger, we extend the one-loop χ PT corrections to lattice gauge theory with heavy-light mesons composed of staggered fermions for both quarks. Putting everything together, we obtain a practical formula to describe all-staggered heavy-light meson masses in terms of quark masses as well as some lattice artifacts related to staggered fermions. In a companion paper, we use this function to analyze lattice-QCD data and extract quark masses and some matrix elements defined in heavy-quark effective theory.

Renormalization of Supersymmetric QCD on the Lattice

NASA Astrophysics Data System (ADS)

Costa, Marios; Panagopoulos, Haralambos

2018-03-01

We perform a pilot study of the perturbative renormalization of a Supersymmetric gauge theory with matter fields on the lattice. As a specific example, we consider Supersymmetric N=1 QCD (SQCD). We study the self-energies of all particles which appear in this theory, as well as the renormalization of the coupling constant. To this end we compute, perturbatively to one-loop, the relevant two-point and three-point Green's functions using both dimensional and lattice regularizations. Our lattice formulation involves theWilson discretization for the gluino and quark fields; for gluons we employ the Wilson gauge action; for scalar fields (squarks) we use naive discretization. The gauge group that we consider is SU(Nc), while the number of colors, Nc, the number of flavors, Nf, and the gauge parameter, α, are left unspecified. We obtain analytic expressions for the renormalization factors of the coupling constant (Zg) and of the quark (ZΨ), gluon (Zu), gluino (Zλ), squark (ZA±), and ghost (Zc) fields on the lattice. We also compute the critical values of the gluino, quark and squark masses. Finally, we address the mixing which occurs among squark degrees of freedom beyond tree level: we calculate the corresponding mixing matrix which is necessary in order to disentangle the components of the squark field via an additional finite renormalization.

Collinearly-improved BK evolution meets the HERA data

DOE PAGES

Iancu, E.; Madrigal, J. D.; Mueller, A. H.; ...

2015-10-03

In a previous publication, we have established a collinearly-improved version of the Balitsky–Kovchegov (BK) equation, which resums to all orders the radiative corrections enhanced by large double transverse logarithms. Here, we study the relevance of this equation as a tool for phenomenology, by confronting it to the HERA data. To that aim, we first improve the perturbative accuracy of our resummation, by including two classes of single-logarithmic corrections: those generated by the first non-singular terms in the DGLAP splitting functions and those expressing the one-loop running of the QCD coupling. The equation thus obtained includes all the next-to-leading order correctionsmore » to the BK equation which are enhanced by (single or double) collinear logarithms. Furthermore, we then use numerical solutions to this equation to fit the HERA data for the electron–proton reduced cross-section at small Bjorken x. We obtain good quality fits for physically acceptable initial conditions. Our best fit, which shows a good stability up to virtualities as large as Q 2 = 400 GeV 2 for the exchanged photon, uses as an initial condition the running-coupling version of the McLerran–Venugopalan model, with the QCD coupling running according to the smallest dipole prescription.« less

Relations between heavy-light meson and quark masses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brambilla, N.; Komijani, J.; Kronfeld, A. S.

Here, the study of heavy-light meson masses should provide a way to determine renormalized quark masses and other properties of heavy-light mesons. In the context of lattice QCD, for example, it is possible to calculate hadronic quantities for arbitrary values of the quark masses. In this paper, we address two aspects relating heavy-light meson masses to the quark masses. First, we introduce a definition of the renormalized quark mass that is free of both scale dependence and renormalon ambiguities, and discuss its relation to more familiar definitions of the quark mass. We then show how this definition enters a mergermore » of the descriptions of heavy-light masses in heavy-quark effective theory and in chiral perturbation theory (χPT). For practical implementations of this merger, we extend the one-loop χPT corrections to lattice gauge theory with heavy-light mesons composed of staggered fermions for both quarks. Putting everything together, we obtain a practical formula to describe all-staggered heavy-light meson masses in terms of quark masses as well as some lattice artifacts related to staggered fermions. In a companion paper, we use this function to analyze lattice-QCD data and extract quark masses and some matrix elements defined in heavy-quark effective theory.« less

Supersymmetric QCD on the lattice: An exploratory study

NASA Astrophysics Data System (ADS)

Costa, M.; Panagopoulos, H.

2017-08-01

We perform a pilot study of the perturbative renormalization of a supersymmetric gauge theory with matter fields on the lattice. As a specific example, we consider supersymmetric N =1 QCD (SQCD). We study the self-energies of all particles which appear in this theory, as well as the renormalization of the coupling constant. To this end we compute, perturbatively to one-loop, the relevant two-point and three-point Green's functions using both dimensional and lattice regularizations. Our lattice formulation involves the Wilson discretization for the gluino and quark fields; for gluons we employ the Wilson gauge action; for scalar fields (squarks) we use naïve discretization. The gauge group that we consider is S U (Nc), while the number of colors, Nc, the number of flavors, Nf, and the gauge parameter, α , are left unspecified. We obtain analytic expressions for the renormalization factors of the coupling constant (Zg) and of the quark (Zψ), gluon (Zu), gluino (Zλ), squark (ZA ±), and ghost (Zc) fields on the lattice. We also compute the critical values of the gluino, quark and squark masses. Finally, we address the mixing which occurs among squark degrees of freedom beyond tree level: we calculate the corresponding mixing matrix which is necessary in order to disentangle the components of the squark field via an additional finite renormalization.

Relations between heavy-light meson and quark masses

DOE PAGES

Brambilla, N.; Komijani, J.; Kronfeld, A. S.; ...

2018-02-07

Here, the study of heavy-light meson masses should provide a way to determine renormalized quark masses and other properties of heavy-light mesons. In the context of lattice QCD, for example, it is possible to calculate hadronic quantities for arbitrary values of the quark masses. In this paper, we address two aspects relating heavy-light meson masses to the quark masses. First, we introduce a definition of the renormalized quark mass that is free of both scale dependence and renormalon ambiguities, and discuss its relation to more familiar definitions of the quark mass. We then show how this definition enters a mergermore » of the descriptions of heavy-light masses in heavy-quark effective theory and in chiral perturbation theory (χPT). For practical implementations of this merger, we extend the one-loop χPT corrections to lattice gauge theory with heavy-light mesons composed of staggered fermions for both quarks. Putting everything together, we obtain a practical formula to describe all-staggered heavy-light meson masses in terms of quark masses as well as some lattice artifacts related to staggered fermions. In a companion paper, we use this function to analyze lattice-QCD data and extract quark masses and some matrix elements defined in heavy-quark effective theory.« less

Secondary structural analyses of ITS1 in Paramecium.

PubMed

Hoshina, Ryo

2010-01-01

The nuclear ribosomal RNA gene operon is interrupted by internal transcribed spacer (ITS) 1 and ITS2. Although the secondary structure of ITS2 has been widely investigated, less is known about ITS1 and its structure. In this study, the secondary structure of ITS1 sequences for Paramecium and other ciliates was predicted. Each Paramecium ITS1 forms an open loop with three helices, A through C. Helix B was highly conserved among Paramecium, and similar helices were found in other ciliates. A phylogenetic analysis using the ITS1 sequences showed high-resolution, implying that ITS1 is a good tool for species-level analyses.

Domain wall network as QCD vacuum: confinement, chiral symmetry, hadronization

NASA Astrophysics Data System (ADS)

Nedelko, Sergei N.; Voronin, Vladimir V.

2017-03-01

An approach to QCD vacuum as a medium describable in terms of statistical ensemble of almost everywhere homogeneous Abelian (anti-)self-dual gluon fields is reviewed. These fields play the role of the confining medium for color charged fields as well as underline the mechanism of realization of chiral SUL(Nf) × SUR(Nf) and UA(1) symmetries. Hadronization formalism based on this ensemble leads to manifestly defined quantum effective meson action. Strong, electromagnetic and weak interactions of mesons are represented in the action in terms of nonlocal n-point interaction vertices given by the quark-gluon loops averaged over the background ensemble. Systematic results for the mass spectrum and decay constants of radially excited light, heavy-light mesons and heavy quarkonia are presented. Relationship of this approach to the results of functional renormalization group and Dyson-Schwinger equations, and the picture of harmonic confinement is briefly outlined.

Octet baryon masses and sigma terms from an SU(3) chiral extrapolation

NASA Astrophysics Data System (ADS)

Young, R. D.; Thomas, A. W.

2010-01-01

We report an analysis of the impressive new lattice simulation results for octet baryon masses in 2+1-flavor QCD. The analysis is based on a low-order expansion about the chiral SU(3) limit in which the symmetry breaking arises from terms linear in the quark masses plus the variation of the Goldstone boson masses in the leading chiral loops. The baryon masses evaluated at the physical light-quark masses are in remarkable agreement with the experimental values, with a model dependence considerably smaller than the rather small statistical uncertainty. From the mass formulas one can evaluate the sigma commutators for all octet baryons. This yields an accurate value for the pion-nucleon sigma commutator. It also yields the first determination of the strangeness sigma term based on 2+1-flavor lattice QCD and, in general, the sigma commutators provide a resolution to the difficult issue of fine-tuning the strange-quark mass.

Three-body decays B →ϕ (ρ )K γ in perturbative QCD approach

NASA Astrophysics Data System (ADS)

Wang, Chao; Liu, Jing-Bin; Li, Hsiang-nan; Lü, Cai-Dian

2018-02-01

We study the three-body radiative decays B →ϕ (ρ )K γ induced by a flavor-changing neutral current in the perturbative QCD approach. Pseudoscalar-vector (P V ) distribution amplitudes (DAs) are introduced for the final-state ϕ K (ρ K ) pair to capture important infrared dynamics in the region with a small P V -pair invariant mass. The dependence of these P V DAs on the parton momentum fraction is parametrized in terms of the Gegenbauer polynomials, and the dependence on the meson momentum fraction is derived through their normalizations to timelike P V form factors. In addition to the dominant electromagnetic penguin, the subleading chromomagnetic penguin, quark-loop and annihilation diagrams are also calculated. After determining the P V DAs from relevant branching-ratio data, the direct C P asymmetries and decay spectra in the P V -pair invariant mass are predicted for each B →ϕ (ρ )K γ mode.

Are the dressed gluon and ghost propagators in the Landau gauge presently determined in the confinement regime of QCD?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pennington, M. R.; Wilson, D. J.

2011-11-01

The gluon and ghost propagators in Landau gauge QCD are investigated using the Schwinger-Dyson equation approach. Working in Euclidean spacetime, we solve for these propagators using a selection of vertex inputs, initially for the ghost equation alone and then for both propagators simultaneously. The results are shown to be highly sensitive to the choices of vertices. We favor the infrared finite ghost solution from studying the ghost equation alone where we argue for a specific unique solution. In order to solve this simultaneously with the gluon using a dressed-one-loop truncation, we find that a nontrivial full ghost-gluon vertex is requiredmore » in the vanishing gluon momentum limit. The self-consistent solutions we obtain correspond to having a masslike term in the gluon propagator dressing, in agreement with similar studies supporting the long-held proposal of Cornwall.« less

Parton distributions and lattice QCD calculations: A community white paper

NASA Astrophysics Data System (ADS)

Lin, Huey-Wen; Nocera, Emanuele R.; Olness, Fred; Orginos, Kostas; Rojo, Juan; Accardi, Alberto; Alexandrou, Constantia; Bacchetta, Alessandro; Bozzi, Giuseppe; Chen, Jiunn-Wei; Collins, Sara; Cooper-Sarkar, Amanda; Constantinou, Martha; Del Debbio, Luigi; Engelhardt, Michael; Green, Jeremy; Gupta, Rajan; Harland-Lang, Lucian A.; Ishikawa, Tomomi; Kusina, Aleksander; Liu, Keh-Fei; Liuti, Simonetta; Monahan, Christopher; Nadolsky, Pavel; Qiu, Jian-Wei; Schienbein, Ingo; Schierholz, Gerrit; Thorne, Robert S.; Vogelsang, Werner; Wittig, Hartmut; Yuan, C.-P.; Zanotti, James

2018-05-01

In the framework of quantum chromodynamics (QCD), parton distribution functions (PDFs) quantify how the momentum and spin of a hadron are divided among its quark and gluon constituents. Two main approaches exist to determine PDFs. The first approach, based on QCD factorization theorems, realizes a QCD analysis of a suitable set of hard-scattering measurements, often using a variety of hadronic observables. The second approach, based on first-principle operator definitions of PDFs, uses lattice QCD to compute directly some PDF-related quantities, such as their moments. Motivated by recent progress in both approaches, in this document we present an overview of lattice-QCD and global-analysis techniques used to determine unpolarized and polarized proton PDFs and their moments. We provide benchmark numbers to validate present and future lattice-QCD calculations and we illustrate how they could be used to reduce the PDF uncertainties in current unpolarized and polarized global analyses. This document represents a first step towards establishing a common language between the two communities, to foster dialogue and to further improve our knowledge of PDFs.

Extension of the HAL QCD approach to inelastic and multi-particle scatterings in lattice QCD

NASA Astrophysics Data System (ADS)

Aoki, S.

We extend the HAL QCD approach, with which potentials between two hadrons can be obtained in QCD at energy below inelastic thresholds, to inelastic and multi-particle scatterings. We first derive asymptotic behaviors of the Nambu-Bethe-Salpeter (NBS) wave function at large space separations for systems with more than 2 particles, in terms of the one-shell $T$-matrix consrainted by the unitarity of quantum field theories. We show that its asymptotic behavior contains phase shifts and mixing angles of $n$ particle scatterings. This property is one of the essential ingredients of the HAL QCD scheme to define "potential" from the NBS wave function in quantum field theories such as QCD. We next construct energy independent but non-local potentials above inelastic thresholds, in terms of these NBS wave functions. We demonstrate an existence of energy-independent coupled channel potentials with a non-relativistic approximation, where momenta of all particles are small compared with their own masses. Combining these two results, we can employ the HAL QCD approach also to investigate inelastic and multi-particle scatterings.

Three-particle N π π state contribution to the nucleon two-point function in lattice QCD

NASA Astrophysics Data System (ADS)

Bär, Oliver

2018-05-01

The three-particle N π π state contribution to the QCD two-point function of standard nucleon interpolating fields is computed to leading order in chiral perturbation theory. Using the experimental values for two low-energy coefficients, the impact of this contribution on lattice QCD calculations of the nucleon mass is estimated. The impact is found to be at the per mille level at most and negligible in practice.

Electroproduction of Eta Mesons in the S11(1535) Resonance Region at High Momentum Transfer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dalton, Mark; Adams, Gary; Ahmidouch, Abdellah

2009-01-01

The differential cross-section for the process p(e,e'p)eta has been measured at Q2 ~ 5.7 and 7.0 (GeV/c)2 for centre-of-mass energies from threshold to 1.8 GeV, encompassing the S11(1535) resonance, which dominates the channel. This is the highest momentum transfer measurement of this exclusive process to date. The helicity-conserving transition amplitude A_1/2, for the production of the S11(1535) resonance, is extracted from the data. This quantity appears to begin scaling as 1/Q3, a predicted signal of the dominance of perturbative QCD, at Q2 ~ 5 (GeV/c)2.

DOE Office of Scientific and Technical Information (OSTI.GOV)

MAEZAWA,Y.; AOKI, S.; EJIRI, S.

The authors report the current status of the systematic studies of the QCD thermodynamics by lattice QCD simulations with two flavors of improved Wilson quarks. They evaluate the critical temperature of two flavor QCD in the chiral limit at zero chemical potential and show the preliminary result. Also they discuss fluctuations at none-zero temperature and density by calculating the quark number and isospin susceptibilities and their derivatives with respect to chemical potential.

A minimal approach to the scattering of physical massless bosons

NASA Astrophysics Data System (ADS)

Boels, Rutger H.; Luo, Hui

2018-05-01

Tree and loop level scattering amplitudes which involve physical massless bosons are derived directly from physical constraints such as locality, symmetry and unitarity, bypassing path integral constructions. Amplitudes can be projected onto a minimal basis of kinematic factors through linear algebra, by employing four dimensional spinor helicity methods or at its most general using projection techniques. The linear algebra analysis is closely related to amplitude relations, especially the Bern-Carrasco-Johansson relations for gluon amplitudes and the Kawai-Lewellen-Tye relations between gluons and graviton amplitudes. Projection techniques are known to reduce the computation of loop amplitudes with spinning particles to scalar integrals. Unitarity, locality and integration-by-parts identities can then be used to fix complete tree and loop amplitudes efficiently. The loop amplitudes follow algorithmically from the trees. A number of proof-of-concept examples are presented. These include the planar four point two-loop amplitude in pure Yang-Mills theory as well as a range of one loop amplitudes with internal and external scalars, gluons and gravitons. Several interesting features of the results are highlighted, such as the vanishing of certain basis coefficients for gluon and graviton amplitudes. Effective field theories are naturally and efficiently included into the framework. Dimensional regularisation is employed throughout; different regularisation schemes are worked out explicitly. The presented methods appear most powerful in non-supersymmetric theories in cases with relatively few legs, but with potentially many loops. For instance, in the introduced approach iterated unitarity cuts of four point amplitudes for non-supersymmetric gauge and gravity theories can be computed by matrix multiplication, generalising the so-called rung-rule of maximally supersymmetric theories. The philosophy of the approach to kinematics also leads to a technique to control colour quantum numbers of scattering amplitudes with matter, especially efficient in the adjoint and fundamental representations.

DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation

PubMed Central

Boedicker, James Q.; Garcia, Hernan G.; Johnson, Stephanie; Phillips, Rob

2014-01-01

As the chief informational molecule of life, DNA is subject to extensive physical manipulations. The energy required to deform double-helical DNA depends on sequence, and this mechanical code of DNA influences gene regulation, such as through nucleosome positioning. Here we examine the sequence-dependent flexibility of DNA in bacterial transcription factor-mediated looping, a context for which the role of sequence remains poorly understood. Using a suite of synthetic constructs repressed by the Lac repressor and two well-known sequences that show large flexibility differences in vitro, we make precise statistical mechanical predictions as to how DNA sequence influences loop formation and test these predictions using in vivo transcription and in vitro single-molecule assays. Surprisingly, sequence-dependent flexibility does not affect in vivo gene regulation. By theoretically and experimentally quantifying the relative contributions of sequence and the DNA-bending protein HU to DNA mechanical properties, we reveal that bending by HU dominates DNA mechanics and masks intrinsic sequence-dependent flexibility. Such a quantitative understanding of how mechanical regulatory information is encoded in the genome will be a key step towards a predictive understanding of gene regulation at single-base pair resolution. PMID:24231252

Using Magnetic Helicity Diagnostics to Determine the Nature of Solar Active-Region Formation

NASA Astrophysics Data System (ADS)

Georgoulis, Manolis K.

Employing a novel nonlinear force-free (NLFF) method that self-consistently infers instantaneous free magnetic-energy and relative magnetic-helicity budgets from single photospheric vector magnetograms, we recently constructed the magnetic energy-helicity (EH) diagram of solar active regions. The EH diagram implies dominant relative helicities of left-handed or right-handed chiralities for the great majority of active regions. The amplitude (budget) of these helicities scales monotonically with the free magnetic energy. This constructive, strongly preferential accumulation of a certain sense of magnetic helicity seems to disqualify recently proposed mechanisms relying on a largely random near-surface convection for the formation of the great majority of active regions. The existing qualitative formation mechanism for these regions remains the conventional Omega-loop emergence following a buoyant ascension from the bottom of the convection zone. However, exceptions to this rule include even eruptive active regions: NOAA AR 11283 is an obvious outlier to the EH diagram, involving significant free magnetic energy with a small relative magnetic helicity. Relying on a timeseries of vector magnetograms of this region, our methodology shows nearly canceling amounts of both senses of helicity and an overall course from a weakly left-handed to a weakly right-handed structure, in the course of which a major eruption occurs. For this and similarly behaving active regions the latest near-surface formation scenario might conceivably be employed successfully. Research partially supported by the EU Seventh Framework Programme under grant agreement No. PIRG07-GA-2010-268245 and by the European Union Social Fund (ESF) and Greek national funds through the Operational Program "Education and Lifelong Learning" of the National Strategic Reference Framework (NSRF) - Research Funding Program: Thales. Investing in knowledge society through the European Social Fund.

QCD In Extreme Conditions

NASA Astrophysics Data System (ADS)

Wilczek, Frank

Introduction Symmetry and the Phenomena of QCD Apparent and Actual Symmetries Asymptotic Freedom Confinement Chiral Symmetry Breaking Chiral Anomalies and Instantons High Temperature QCD: Asymptotic Properties Significance of High Temperature QCD Numerical Indications for Quasi-Free Behavior Ideas About Quark-Gluon Plasma Screening Versus Confinement Models of Chiral Symmetry Breaking More Refined Numerical Experiments High-Temperature QCD: Phase Transitions Yoga of Phase Transitions and Order Parameters Application to Glue Theories Application to Chiral Transitions Close Up on Two Flavors A Genuine Critical Point! (?) High-Density QCD: Methods Hopes, Doubts, and Fruition Another Renormalization Group Pairing Theory Taming the Magnetic Singularity High-Density QCD: Color-Flavor Locking and Quark-Hadron Continuity Gauge Symmetry (Non)Breaking Symmetry Accounting Elementary Excitations A Modified Photon Quark-Hadron Continuity Remembrance of Things Past More Quarks Fewer Quarks and Reality

Role of CBS and Bateman Domains in Phosphorylation-Dependent Regulation of a CLC Anion Channel.

PubMed

Yamada, Toshiki; Krzeminski, Mickael; Bozoky, Zoltan; Forman-Kay, Julie D; Strange, Kevin

2016-11-01

Eukaryotic CLC anion channels and transporters are homodimeric proteins composed of multiple α-helical membrane domains and large cytoplasmic C-termini containing two cystathionine-β-synthase domains (CBS1 and CBS2) that dimerize to form a Bateman domain. The Bateman domains of adjacent CLC subunits interact to form a Bateman domain dimer. The functions of CLC CBS and Bateman domains are poorly understood. We utilized the Caenorhabditis elegans CLC-1/2/Ka/Kb anion channel homolog CLH-3b to characterize the regulatory roles of CLC cytoplasmic domains. CLH-3b activity is reduced by phosphorylation or deletion of a 14-amino-acid activation domain (AD) located on the linker connecting CBS1 and CBS2. We demonstrate here that phosphorylation-dependent reductions in channel activity require an intact Bateman domain dimer and concomitant phosphorylation or deletion of both ADs. Regulation of a CLH-3b AD deletion mutant is reconstituted by intracellular perfusion with recombinant 14-amino-acid AD peptides. The sulfhydryl reactive reagent 2-(trimethylammonium)ethyl methanethiosulfonate bromide (MTSET) alters in a phosphorylation-dependent manner the activity of channels containing single cysteine residues that are engineered into the short intracellular loop connecting membrane α-helices H and I (H-I loop), the AD, CBS1, and CBS2. In contrast, MTSET has no effect on channels in which cysteine residues are engineered into intracellular regions that are dispensable for regulation. These studies together with our previous work suggest that binding and unbinding of the AD to the Bateman domain dimer induces conformational changes that are transduced to channel membrane domains via the H-I loop. Our findings provide new, to our knowledge, insights into the roles of CLC Bateman domains and the structure-function relationships that govern the regulation of CLC protein activity by diverse ligands and signaling pathways. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

A predictive model of asymmetric morphogenesis from 3D reconstructions of mouse heart looping dynamics

PubMed Central

Le Garrec, Jean-François; Ivanovitch, Kenzo D; Raphaël, Etienne; Bangham, J Andrew; Torres, Miguel; Coen, Enrico; Mohun, Timothy J

2017-01-01

How left-right patterning drives asymmetric morphogenesis is unclear. Here, we have quantified shape changes during mouse heart looping, from 3D reconstructions by HREM. In combination with cell labelling and computer simulations, we propose a novel model of heart looping. Buckling, when the cardiac tube grows between fixed poles, is modulated by the progressive breakdown of the dorsal mesocardium. We have identified sequential left-right asymmetries at the poles, which bias the buckling in opposite directions, thus leading to a helical shape. Our predictive model is useful to explore the parameter space generating shape variations. The role of the dorsal mesocardium was validated in Shh-/- mutants, which recapitulate heart shape changes expected from a persistent dorsal mesocardium. Our computer and quantitative tools provide novel insight into the mechanism of heart looping and the contribution of different factors, beyond the simple description of looping direction. This is relevant to congenital heart defects. PMID:29179813

A curved RNA helix incorporating an internal loop with G·A and A·A non-Watson–Crick base pairing

PubMed Central

Baeyens, Katrien J.; De Bondt, Hendrik L.; Pardi, Arthur; Holbrook, Stephen R.

1996-01-01

The crystal structure of the RNA dodecamer 5′-GGCC(GAAA)GGCC-3′ has been determined from x-ray diffraction data to 2.3-Å resolution. In the crystal, these oligomers form double helices around twofold symmetry axes. Four consecutive non-Watson–Crick base pairs make up an internal loop in the middle of the duplex, including sheared G·A pairs and novel asymmetric A·A pairs. This internal loop sequence produces a significant curvature and narrowing of the double helix. The helix is curved by 34° from end to end and the diameter is narrowed by 24% in the internal loop. A Mn2+ ion is bound directly to the N7 of the first guanine in the Watson–Crick region following the internal loop and the phosphate of the preceding residue. This Mn2+ location corresponds to a metal binding site observed in the hammerhead catalytic RNA. PMID:8917508

QCD dirac operator at nonzero chemical potential: lattice data and matrix model.

PubMed

Akemann, Gernot; Wettig, Tilo

2004-03-12

Recently, a non-Hermitian chiral random matrix model was proposed to describe the eigenvalues of the QCD Dirac operator at nonzero chemical potential. This matrix model can be constructed from QCD by mapping it to an equivalent matrix model which has the same symmetries as QCD with chemical potential. Its microscopic spectral correlations are conjectured to be identical to those of the QCD Dirac operator. We investigate this conjecture by comparing large ensembles of Dirac eigenvalues in quenched SU(3) lattice QCD at a nonzero chemical potential to the analytical predictions of the matrix model. Excellent agreement is found in the two regimes of weak and strong non-Hermiticity, for several different lattice volumes.

Pivotal role of extended linker 2 in the activation of Gα by G protein-coupled receptor.

PubMed

Huang, Jianyun; Sun, Yutong; Zhang, J Jillian; Huang, Xin-Yun

2015-01-02

G protein-coupled receptors (GPCRs) relay extracellular signals mainly to heterotrimeric G-proteins (Gαβγ) and they are the most successful drug targets. The mechanisms of G-protein activation by GPCRs are not well understood. Previous studies have revealed a signal relay route from a GPCR via the C-terminal α5-helix of Gα to the guanine nucleotide-binding pocket. Recent structural and biophysical studies uncover a role for the opening or rotating of the α-helical domain of Gα during the activation of Gα by a GPCR. Here we show that β-adrenergic receptors activate eight Gαs mutant proteins (from a screen of 66 Gαs mutants) that are unable to bind Gβγ subunits in cells. Five of these eight mutants are in the αF/Linker 2/β2 hinge region (extended Linker 2) that connects the Ras-like GTPase domain and the α-helical domain of Gαs. This extended Linker 2 is the target site of a natural product inhibitor of Gq. Our data show that the extended Linker 2 is critical for Gα activation by GPCRs. We propose that a GPCR via its intracellular loop 2 directly interacts with the β2/β3 loop of Gα to communicate to Linker 2, resulting in the opening and closing of the α-helical domain and the release of GDP during G-protein activation. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Pressure response of protein backbone structure. Pressure-induced amide 15N chemical shifts in BPTI.

PubMed Central

Akasaka, K.; Li, H.; Yamada, H.; Li, R.; Thoresen, T.; Woodward, C. K.

1999-01-01

The effect of pressure on amide 15N chemical shifts was studied in uniformly 15N-labeled basic pancreatic trypsin inhibitor (BPTI) in 90%1H2O/10%2H2O, pH 4.6, by 1H-15N heteronuclear correlation spectroscopy between 1 and 2,000 bar. Most 15N signals were low field shifted linearly and reversibly with pressure (0.468 +/- 0.285 ppm/2 kbar), indicating that the entire polypeptide backbone structure is sensitive to pressure. A significant variation of shifts among different amide groups (0-1.5 ppm/2 kbar) indicates a heterogeneous response throughout within the three-dimensional structure of the protein. A tendency toward low field shifts is correlated with a decrease in hydrogen bond distance on the order of 0.03 A/2 kbar for the bond between the amide nitrogen atom and the oxygen atom of either carbonyl or water. The variation of 15N shifts is considered to reflect site-specific changes in phi, psi angles. For beta-sheet residues, a decrease in psi angles by 1-2 degrees/2 kbar is estimated. On average, shifts are larger for helical and loop regions (0.553 +/- 0.343 and 0.519 +/- 0.261 ppm/2 kbar, respectively) than for beta-sheet (0.295 +/- 0.195 ppm/2 kbar), suggesting that the pressure-induced structural changes (local compressibilities) are larger in helical and loop regions than in beta-sheet. Because compressibility is correlated with volume fluctuation, the result is taken to indicate that the volume fluctuation is larger in helical and loop regions than in beta-sheet. An important aspect of the volume fluctuation inferred from pressure shifts is that they include motions in slower time ranges (less than milliseconds) in which many biological processes may take place. PMID:10548039

Standard model light-by-light scattering in SANC: Analytic and numeric evaluation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bardin, D. Yu., E-mail: bardin@nu.jinr.ru; Kalinovskaya, L. V., E-mail: kalinov@nu.jinr.ru; Uglov, E. D., E-mail: corner@nu.jinr.r

2010-11-15

The implementation of the Standard Model process {gamma}{gamma} {yields} {gamma}{gamma} through a fermion and boson loop into the framework of SANC system and additional precomputation modules used for calculation of massive box diagrams are described. The computation of this process takes into account nonzero mass of loop particles. The covariant and helicity amplitudes for this process, some particular cases of D{sub 0} and C{sub 0} Passarino-Veltman functions, and also numerical results of corresponding SANC module evaluation are presented. Whenever possible, the results are compared with those existing in the literature.

The generalized scheme-independent Crewther relation in QCD

NASA Astrophysics Data System (ADS)

Shen, Jian-Ming; Wu, Xing-Gang; Ma, Yang; Brodsky, Stanley J.

2017-07-01

The Principle of Maximal Conformality (PMC) provides a systematic way to set the renormalization scales order-by-order for any perturbative QCD calculable processes. The resulting predictions are independent of the choice of renormalization scheme, a requirement of renormalization group invariance. The Crewther relation, which was originally derived as a consequence of conformally invariant field theory, provides a remarkable connection between two observables when the β function vanishes: one can show that the product of the Bjorken sum rule for spin-dependent deep inelastic lepton-nucleon scattering times the Adler function, defined from the cross section for electron-positron annihilation into hadrons, has no pQCD radiative corrections. The ;Generalized Crewther Relation; relates these two observables for physical QCD with nonzero β function; specifically, it connects the non-singlet Adler function (Dns) to the Bjorken sum rule coefficient for polarized deep-inelastic electron scattering (CBjp) at leading twist. A scheme-dependent ΔCSB-term appears in the analysis in order to compensate for the conformal symmetry breaking (CSB) terms from perturbative QCD. In conventional analyses, this normally leads to unphysical dependence in both the choice of the renormalization scheme and the choice of the initial scale at any finite order. However, by applying PMC scale-setting, we can fix the scales of the QCD coupling unambiguously at every order of pQCD. The result is that both Dns and the inverse coefficient CBjp-1 have identical pQCD coefficients, which also exactly match the coefficients of the corresponding conformal theory. Thus one obtains a new generalized Crewther relation for QCD which connects two effective charges, αˆd (Q) =∑i≥1 αˆg1 i (Qi), at their respective physical scales. This identity is independent of the choice of the renormalization scheme at any finite order, and the dependence on the choice of the initial scale is negligible. Similar scale-fixed commensurate scale relations also connect other physical observables at their physical momentum scales, thus providing convention-independent, fundamental precision tests of QCD.

Dislocation dynamics simulations of interactions between gliding dislocations and radiation induced prismatic loops in zirconium

NASA Astrophysics Data System (ADS)

Drouet, Julie; Dupuy, Laurent; Onimus, Fabien; Mompiou, Frédéric; Perusin, Simon; Ambard, Antoine

2014-06-01

The mechanical behavior of Pressurized Water Reactor fuel cladding tubes made of zirconium alloys is strongly affected by neutron irradiation due to the high density of radiation induced dislocation loops. In order to investigate the interaction mechanisms between gliding dislocations and loops in zirconium, a new nodal dislocation dynamics code, adapted to Hexagonal Close Packed metals, has been used. Various configurations have been systematically computed considering different glide planes, basal or prismatic, and different characters, edge or screw, for gliding dislocations with -type Burgers vectors. Simulations show various interaction mechanisms such as (i) absorption of a loop on an edge dislocation leading to the formation of a double super-jog, (ii) creation of a helical turn, on a screw dislocation, that acts as a strong pinning point or (iii) sweeping of a loop by a gliding dislocation. It is shown that the clearing of loops is more favorable when the dislocation glides in the basal plane than in the prismatic plane explaining the easy dislocation channeling in the basal plane observed after neutron irradiation by transmission electron microscopy.

Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures.

PubMed

Sloma, Michael F; Mathews, David H

2016-12-01

RNA secondary structure prediction is widely used to analyze RNA sequences. In an RNA partition function calculation, free energy nearest neighbor parameters are used in a dynamic programming algorithm to estimate statistical properties of the secondary structure ensemble. Previously, partition functions have largely been used to estimate the probability that a given pair of nucleotides form a base pair, the conditional stacking probability, the accessibility to binding of a continuous stretch of nucleotides, or a representative sample of RNA structures. Here it is demonstrated that an RNA partition function can also be used to calculate the exact probability of formation of hairpin loops, internal loops, bulge loops, or multibranch loops at a given position. This calculation can also be used to estimate the probability of formation of specific helices. Benchmarking on a set of RNA sequences with known secondary structures indicated that loops that were calculated to be more probable were more likely to be present in the known structure than less probable loops. Furthermore, highly probable loops are more likely to be in the known structure than the set of loops predicted in the lowest free energy structures. © 2016 Sloma and Mathews; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Chimeric microbial rhodopsins for optical activation of Gs-proteins

PubMed Central

Yoshida, Kazuho; Yamashita, Takahiro; Sasaki, Kengo; Inoue, Keiichi; Shichida, Yoshinori; Kandori, Hideki

2017-01-01

We previously showed that the chimeric proteins of microbial rhodopsins, such as light-driven proton pump bacteriorhodopsin (BR) and Gloeobacter rhodopsin (GR) that contain cytoplasmic loops of bovine rhodopsin, are able to activate Gt protein upon light absorption. These facts suggest similar protein structural changes in both the light-driven proton pump and animal rhodopsin. Here we report two trials to engineer chimeric rhodopsins, one for the inserted loop, and another for the microbial rhodopsin template. For the former, we successfully activated Gs protein by light through the incorporation of the cytoplasmic loop of β2-adrenergic receptor (β2AR). For the latter, we did not observe any G-protein activation for the light-driven sodium pump from Indibacter alkaliphilus (IndiR2) or a light-driven chloride pump halorhodopsin from Natronomonas pharaonis (NpHR), whereas the light-driven proton pump GR showed light-dependent G-protein activation. This fact suggests that a helix opening motion is common to G protein coupled receptor (GPCR) and GR, but not to IndiR2 and NpHR. Light-induced difference FTIR spectroscopy revealed similar structural changes between WT and the third loop chimera for each light-driven pump. A helical structural perturbation, which was largest for GR, was further enhanced in the chimera. We conclude that similar structural dynamics that occur on the cytoplasmic side of GPCR are needed to design chimeric microbial rhodopsins. PMID:29362703

QCD as a Theory of Hadrons

NASA Astrophysics Data System (ADS)

Narison, Stephan

2004-05-01

About Stephan Narison; Outline of the book; Preface; Acknowledgements; Part I. General Introduction: 1. A short flash on particle physics; 2. The pre-QCD era; 3. The QCD story; 4. Field theory ingredients; Part II. QCD Gauge Theory: 5. Lagrangian and gauge invariance; 6. Quantization using path integral; 7. QCD and its global invariance; Part III. MS scheme for QCD and QED: Introduction; 8. Dimensional regularization; 9. The MS renormalization scheme; 10. Renormalization of operators using the background field method; 11. The renormalization group; 12. Other renormalization schemes; 13. MS scheme for QED; 14. High-precision low-energy QED tests; Part IV. Deep Inelastic Scattering at Hadron Colliders: 15. OPE for deep inelastic scattering; 16. Unpolarized lepton-hadron scattering; 17. The Altarelli-Parisi equation; 18. More on unpolarized deep inelastic scatterings; 19. Polarized deep-inelastic processes; 20. Drell-Yan process; 21. One 'prompt photon' inclusive production; Part V. Hard Processes in e+e- Collisions: Introduction; 22. One hadron inclusive production; 23. gg scatterings and the 'spin' of the photon; 24. QCD jets; 25. Total inclusive hadron productions; Part VI. Summary of QCD Tests and as Measurements; Part VII. Power Corrections in QCD: 26. Introduction; 27. The SVZ expansion; 28. Technologies for evaluating Wilson coefficients; 29. Renormalons; 30. Beyond the SVZ expansion; Part VIII. QCD Two-Point Functions: 31. References guide to original works; 32. (Pseudo)scalar correlators; 33. (Axial-)vector two-point functions; 34. Tensor-quark correlator; 35. Baryonic correlators; 36. Four-quark correlators; 37. Gluonia correlators; 38. Hybrid correlators; 39. Correlators in x-space; Part IX. QCD Non-Perturbative Methods: 40. Introduction; 41. Lattice gauge theory; 42. Chiral perturbation theory; 43. Models of the QCD effective action; 44. Heavy quark effective theory; 45. Potential approaches to quarkonia; 46. On monopole and confinement; Part X. QCD Spectral Sum Rules: 47. Introduction; 48. Theoretical foundations; 49. Survey of QCD spectral sum rules; 50. Weinberg and DMO sum rules; 51. The QCD coupling as; 52. The QCD condensates; 53. Light and heavy quark masses, etc.; 54. Hadron spectroscopy; 55. D, B and Bc exclusive weak decays; 56. B0(s)-B0(s) mixing, kaon CP violation; 57. Thermal behaviour of QCD; 58. More on spectral sum rules; Part XI. Appendix A: physical constants and unites; Appendix B: weight factors for SU(N)c; Appendix C: coordinates and momenta; Appendix D: Dirac equation and matrices; Appendix E: Feynman rules; Appendix F: Feynman integrals; Appendix G: useful formulae for the sum rules; Bibliography; Index.

QCD as a Theory of Hadrons

NASA Astrophysics Data System (ADS)

Narison, Stephan

2007-07-01

About Stephan Narison; Outline of the book; Preface; Acknowledgements; Part I. General Introduction: 1. A short flash on particle physics; 2. The pre-QCD era; 3. The QCD story; 4. Field theory ingredients; Part II. QCD Gauge Theory: 5. Lagrangian and gauge invariance; 6. Quantization using path integral; 7. QCD and its global invariance; Part III. MS scheme for QCD and QED: Introduction; 8. Dimensional regularization; 9. The MS renormalization scheme; 10. Renormalization of operators using the background field method; 11. The renormalization group; 12. Other renormalization schemes; 13. MS scheme for QED; 14. High-precision low-energy QED tests; Part IV. Deep Inelastic Scattering at Hadron Colliders: 15. OPE for deep inelastic scattering; 16. Unpolarized lepton-hadron scattering; 17. The Altarelli-Parisi equation; 18. More on unpolarized deep inelastic scatterings; 19. Polarized deep-inelastic processes; 20. Drell-Yan process; 21. One 'prompt photon' inclusive production; Part V. Hard Processes in e+e- Collisions: Introduction; 22. One hadron inclusive production; 23. gg scatterings and the 'spin' of the photon; 24. QCD jets; 25. Total inclusive hadron productions; Part VI. Summary of QCD Tests and as Measurements; Part VII. Power Corrections in QCD: 26. Introduction; 27. The SVZ expansion; 28. Technologies for evaluating Wilson coefficients; 29. Renormalons; 30. Beyond the SVZ expansion; Part VIII. QCD Two-Point Functions: 31. References guide to original works; 32. (Pseudo)scalar correlators; 33. (Axial-)vector two-point functions; 34. Tensor-quark correlator; 35. Baryonic correlators; 36. Four-quark correlators; 37. Gluonia correlators; 38. Hybrid correlators; 39. Correlators in x-space; Part IX. QCD Non-Perturbative Methods: 40. Introduction; 41. Lattice gauge theory; 42. Chiral perturbation theory; 43. Models of the QCD effective action; 44. Heavy quark effective theory; 45. Potential approaches to quarkonia; 46. On monopole and confinement; Part X. QCD Spectral Sum Rules: 47. Introduction; 48. Theoretical foundations; 49. Survey of QCD spectral sum rules; 50. Weinberg and DMO sum rules; 51. The QCD coupling as; 52. The QCD condensates; 53. Light and heavy quark masses, etc.; 54. Hadron spectroscopy; 55. D, B and Bc exclusive weak decays; 56. B0(s)-B0(s) mixing, kaon CP violation; 57. Thermal behaviour of QCD; 58. More on spectral sum rules; Part XI. Appendix A: physical constants and unites; Appendix B: weight factors for SU(N)c; Appendix C: coordinates and momenta; Appendix D: Dirac equation and matrices; Appendix E: Feynman rules; Appendix F: Feynman integrals; Appendix G: useful formulae for the sum rules; Bibliography; Index.

Finite-volume and partial quenching effects in the magnetic polarizability of the neutron

NASA Astrophysics Data System (ADS)

Hall, J. M. M.; Leinweber, D. B.; Young, R. D.

2014-03-01

There has been much progress in the experimental measurement of the electric and magnetic polarizabilities of the nucleon. Similarly, lattice QCD simulations have recently produced dynamical QCD results for the magnetic polarizability of the neutron approaching the chiral regime. In order to compare the lattice simulations with experiment, calculation of partial quenching and finite-volume effects is required prior to an extrapolation in quark mass to the physical point. These dependencies are described using chiral effective field theory. Corrections to the partial quenching effects associated with the sea-quark-loop electric charges are estimated by modeling corrections to the pion cloud. These are compared to the uncorrected lattice results. In addition, the behavior of the finite-volume corrections as a function of pion mass is explored. Box sizes of approximately 7 fm are required to achieve a result within 5% of the infinite-volume result at the physical pion mass. A variety of extrapolations are shown at different box sizes, providing a benchmark to guide future lattice QCD calculations of the magnetic polarizabilities. A relatively precise value for the physical magnetic polarizability of the neutron is presented, βn=1.93(11)stat(11)sys×10-4 fm3, which is in agreement with current experimental results.

PREFACE: Focus section on Hadronic Physics Focus section on Hadronic Physics

NASA Astrophysics Data System (ADS)

Roberts, Craig; Swanson, Eric

2007-07-01

Hadronic physics is the study of strongly interacting matter and its underlying theory, Quantum Chromodynamics (QCD). The field had its beginnings after World War Two, when hadrons were discovered in ever increasing numbers. Today, it encompasses topics like the quark-gluon structure of hadrons at varying scales, the quark-gluon plasma and hadronic matter at extreme temperature and density; it also underpins nuclear physics and has significant impact on particle physics, astrophysics, and cosmology. Among the goals of hadronic physics are to determine the parameters of QCD, understand the origin and characteristics of confinement, understand the dynamics and consequences of dynamical chiral symmetry breaking, explore the role of quarks and gluons in nuclei and in matter under extreme conditions and understand the quark and gluon structure of hadrons. In general, the process is one of discerning the relevant degrees of freedom and relating these to the fundamental fields of QCD. The emphasis is on understanding QCD, rather than testing it. The papers gathered in this special focus section of Journal of Physics G: Nuclear and Particle Physics attempt to cover this broad range of subjects. Alkofer and Greensite examine the issue of quark and gluon confinement with the focus on models of the QCD vacuum, lattice gauge theory investigations, and the relationship to the AdS/CFT correspondence postulate. Arrington et al. review nucleon form factors and their role in determining quark orbital momentum, the strangeness content of the nucleon, meson cloud effects, and the transition from nonperturbative to perturbative QCD dynamics. The physics associated with hadronic matter at high temperature and density and at low Bjorken-x at the Relativistic Heavy Ion Collider (RHIC), the SPS at CERN, and at the future LHC is summarized by d'Enterria. The article of Lee and Smith examines experiment and theory associated with electromagnetic meson production from nucleons and illustrates how the structure of the nucleon is revealed. Reimer reviews how the Drell--Yan process can be used to explore the sea quark structure of nucleons, thereby probing such phenomena as flavour asymmetry in the nucleon and nuclear medium modification of nucleon properties. The exploitation of the B factories has led to a resurgence of interest in heavy quark spectroscopy. Concurrently, interest in light quark spectroscopy and gluonic excitations remains high, with several new experimental efforts in the planning or building stages. The current status of all of this is reviewed by Rosner. Finally, Vogelsang summarizes the status of polarized deep inelastic lepton-nucleon scattering experiments at RHIC and their impact on the theoretical understanding of nucleon helicity structure, gluon polarization in the nucleus, and transverse spin asymmetries. Of course, hadronic physics is a much broader subject than can be conveyed in this special focus section; advances in effective field theory, lattice gauge theory, generalised parton distributions and many other subfields are not covered here. Nevertheless, we hope that this focus section will help the reader appreciate the vitality, breadth of endeavour, and the phenomenological richness of hadronic physics.

AdS/QCD and Applications of Light-Front Holography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brodsky, Stanley J.; /SLAC /Southern Denmark U., CP3-Origins; Cao, Fu-Guang

2012-02-16

Light-Front Holography leads to a rigorous connection between hadronic amplitudes in a higher dimensional anti-de Sitter (AdS) space and frame-independent light-front wavefunctions of hadrons in 3 + 1 physical space-time, thus providing a compelling physical interpretation of the AdS/CFT correspondence principle and AdS/QCD, a useful framework which describes the correspondence between theories in a modified AdS5 background and confining field theories in physical space-time. To a first semiclassical approximation, where quantum loops and quark masses are not included, this approach leads to a single-variable light-front Schroedinger equation which determines the eigenspectrum and the light-front wavefunctions of hadrons for general spinmore » and orbital angular momentum. The coordinate z in AdS space is uniquely identified with a Lorentz-invariant coordinate {zeta} which measures the separation of the constituents within a hadron at equal light-front time. The internal structure of hadrons is explicitly introduced and the angular momentum of the constituents plays a key role. We give an overview of the light-front holographic approach to strongly coupled QCD. In particular, we study the photon-to-meson transition form factors (TFFs) F{sub M{gamma}}(Q{sup 2}) for {gamma}{gamma}* {yields} M using light-front holographic methods. The results for the TFFs for the {eta} and {eta}' mesons are also presented. Some novel features of QCD are discussed, including the consequences of confinement for quark and gluon condensates. A method for computing the hadronization of quark and gluon jets at the amplitude level is outlined.« less

Assignment of the sup 1 H and sup 15 N NMR spectra of Rhodobacter capsulatus ferrocytochrome c sub 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gooley, P.R.; Caffrey, M.S.; Cusanovich, M.A.

1990-03-06

The peptide resonances of the {sup 1}H and {sup 15}N nuclear magnetic resonance spectra of ferrocytochrome c{sub 2} from Rhodobacter capsulatus are sequentially assigned by a combination of 2D {sup 1}H-{sup 1}H and {sup 1}H-{sup 15}N spectroscopy, the latter performed on {sup 15}N-enriched protein. Short-range nuclear Overhauser effect (NOE) data show {alpha}-helices from residues 3-17, 55-65, 69-88, and 103-115. Within the latter two {alpha}-helices, there are three single 3{sub 10} turns, 70-72, 76-78, and 107-109. In addition {alpha}H-NH{sub i+1} and {alpha}H-NH{sub i+2} NOEs indicate that the N-terminal helix (3-17) is distorted. Compared to horse or tuna cytochrome c and cytochromemore » c{sub 2} of Rhodospirillium rubrum, there is a 6-residue insertion at residues 23-29 in R. capsulatus cytochrome c{sub 2}. The NOE data show that this insertion forms a loop, probably an {Omega} loop. {sup 1}H-{sup 15}N heteronuclear multiple quantum correlation experiments are used to follow NH exchange over a period of 40 h. As the 2D spectra are acquired in short time periods (30 min), rates for intermediate exchanging protons can be measured. Comparison of the NH exchange data for the N-terminal helix of cytochrome c{sub 2} of R. capsulatus with the highly homologous horse heart cytochrome c shows that this helix is less stable in cytochrome c{sub 2}.« less

Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase

PubMed Central

2012-01-01

Background During elongation, multi-subunit RNA polymerases (RNAPs) cycle between phosphodiester bond formation and nucleic acid translocation. In the conformation associated with catalysis, the mobile “trigger loop” of the catalytic subunit closes on the nucleoside triphosphate (NTP) substrate. Closing of the trigger loop is expected to exclude water from the active site, and dehydration may contribute to catalysis and fidelity. In the absence of a NTP substrate in the active site, the trigger loop opens, which may enable translocation. Another notable structural element of the RNAP catalytic center is the “bridge helix” that separates the active site from downstream DNA. The bridge helix may participate in translocation by bending against the RNA/DNA hybrid to induce RNAP forward movement and to vacate the active site for the next NTP loading. The transition between catalytic and translocation conformations of RNAP is not evident from static crystallographic snapshots in which macromolecular motions may be restrained by crystal packing. Results All atom molecular dynamics simulations of Thermus thermophilus (Tt) RNAP reveal flexible hinges, located within the two helices at the base of the trigger loop, and two glycine hinges clustered near the N-terminal end of the bridge helix. As simulation progresses, these hinges adopt distinct conformations in the closed and open trigger loop structures. A number of residues (described as “switch” residues) trade atomic contacts (ion pairs or hydrogen bonds) in response to changes in hinge orientation. In vivo phenotypes and in vitro activities rendered by mutations in the hinge and switch residues in Saccharomyces cerevisiae (Sc) RNAP II support the importance of conformational changes predicted from simulations in catalysis and translocation. During simulation, the elongation complex with an open trigger loop spontaneously translocates forward relative to the elongation complex with a closed trigger loop. Conclusions Switching between catalytic and translocating RNAP forms involves closing and opening of the trigger loop and long-range conformational changes in the atomic contacts of amino acid side chains, some located at a considerable distance from the trigger loop and active site. Trigger loop closing appears to support chemistry and the fidelity of RNA synthesis. Trigger loop opening and limited bridge helix bending appears to promote forward nucleic acid translocation. PMID:22676913

Key issues in the computational simulation of GPCR function: representation of loop domains

NASA Astrophysics Data System (ADS)

Mehler, E. L.; Periole, X.; Hassan, S. A.; Weinstein, H.

2002-11-01

Some key concerns raised by molecular modeling and computational simulation of functional mechanisms for membrane proteins are discussed and illustrated for members of the family of G protein coupled receptors (GPCRs). Of particular importance are issues related to the modeling and computational treatment of loop regions. These are demonstrated here with results from different levels of computational simulations applied to the structures of rhodopsin and a model of the 5-HT2A serotonin receptor, 5-HT2AR. First, comparative Molecular Dynamics (MD) simulations are reported for rhodopsin in vacuum and embedded in an explicit representation of the membrane and water environment. It is shown that in spite of a partial accounting of solvent screening effects by neutralization of charged side chains, vacuum MD simulations can lead to severe distortions of the loop structures. The primary source of the distortion appears to be formation of artifactual H-bonds, as has been repeatedly observed in vacuum simulations. To address such shortcomings, a recently proposed approach that has been developed for calculating the structure of segments that connect elements of secondary structure with known coordinates, is applied to 5-HT2AR to obtain an initial representation of the loops connecting the transmembrane (TM) helices. The approach consists of a simulated annealing combined with biased scaled collective variables Monte Carlo technique, and is applied to loops connecting the TM segments on both the extra-cellular and the cytoplasmic sides of the receptor. Although this initial calculation treats the loops as independent structural entities, the final structure exhibits a number of interloop interactions that may have functional significance. Finally, it is shown here that in the case where a given loop from two different GPCRs (here rhodopsin and 5-HT2AR) has approximately the same length and some degree of sequence identity, the fold adopted by the loops can be similar. Thus, in such special cases homology modeling might be used to obtain initial structures of these loops. Notably, however, all other loops in these two receptors appear to be very different in sequence and structure, so that their conformations can be found reliably only by ab initio, energy based methods and not by homology modeling.

Stability of flat spacetime in quantum gravity

NASA Astrophysics Data System (ADS)

Jordan, R. D.

1987-12-01

In a previous paper, a modified effective-action formalism was developed which produces equations satisfied by the expectation value of the field, rather than the usual in-out average. Here this formalism is applied to a quantized scalar field in a background which is a small perturbation from Minkowski spacetime. The one-loop effective field equation describes the back reaction of created particles on the gravitational field, and is calculated in this paper to linear order in the perturbation. In this way we rederive an equation first found by Horowitz using completely different methods. This equation possesses exponentially growing solutions, so we confirm Horowitz's conclusion that flat spacetime is unstable in this approximation to the theory. The new derivation shows that the field equation is just as useful as the one-loop approximation to the in-out equation, contrary to earlier arguments. However, the instability suggests that the one-loop approximation cannot be trusted for gravity. These results are compared with the corresponding situation in QED and QCD.

The baryon vector current in the combined chiral and 1/Nc expansions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Flores-Mendieta, Ruben; Goity, Jose L

2014-12-01

The baryon vector current is computed at one-loop order in large-Nc baryon chiral perturbation theory, where Nc is the number of colors. Loop graphs with octet and decuplet intermediate states are systematically incorporated into the analysis and the effects of the decuplet-octet mass difference and SU(3) flavor symmetry breaking are accounted for. There are large-Nc cancellations between different one-loop graphs as a consequence of the large-Nc spin-flavor symmetry of QCD baryons. The results are compared against the available experimental data through several fits in order to extract information about the unknown parameters. The large-Nc baryon chiral perturbation theory predictions aremore » in very good agreement both with the expectations from the 1/Nc expansion and with the experimental data. The effect of SU(3) flavor symmetry breaking for the |Delta S|=1 vector current form factors f1(0) results in a reduction by a few percent with respect to the corresponding SU(3) symmetric values.« less

On the ultimate uncertainty of the top quark pole mass

NASA Astrophysics Data System (ADS)

Beneke, M.; Marquard, P.; Nason, P.; Steinhauser, M.

2017-12-01

We combine the known asymptotic behaviour of the QCD perturbation series expansion, which relates the pole mass of a heavy quark to the MS ‾ mass, with the exact series coefficients up to the four-loop order to determine the ultimate uncertainty of the top-quark pole mass due to the renormalon divergence. We perform extensive tests of our procedure by varying the number of colours and flavours, as well as the scale of the strong coupling and the MS ‾ mass. Including an estimate of the internal bottom and charm quark mass effect, we conclude that this uncertainty is around 110 MeV. We further estimate the additional contribution to the mass relation from the five-loop correction and beyond to be around 300 MeV.

The growth pattern of the human intestine and its mesentery.

PubMed

Soffers, Jelly H M; Hikspoors, Jill P J M; Mekonen, Hayelom K; Koehler, S Eleonore; Lamers, Wouter H

2015-08-22

It remains unclear to what extent midgut rotation determines human intestinal topography and pathology. We reinvestigated the midgut during its looping and herniation phases of development, using novel 3D visualization techniques. We distinguished 3 generations of midgut loops. The topography of primary and secondary loops was constant, but that of tertiary loops not. The orientation of the primary loop changed from sagittal to transverse due to the descent of ventral structures in a body with a still helical body axis. The 1st secondary loop (duodenum, proximal jejunum) developed intraabdominally towards a left-sided position. The 2nd secondary loop (distal jejunum) assumed a left-sided position inside the hernia before returning, while the 3rd and 4th secondary loops retained near-midline positions. Intestinal return into the abdomen resembled a backward sliding movement. Only after return, the 4th secondary loop (distal ileum, cecum) rapidly "slid" into the right lower abdomen. The seemingly random position of the tertiary small-intestinal loops may have a biomechanical origin. The interpretation of "intestinal rotation" as a mechanistic rather than a descriptive concept underlies much of the confusion accompanying the physiological herniation. We argue, instead, that the concept of "en-bloc rotation" of the developing midgut is a fallacy of schematic drawings. Primary, secondary and tertiary loops arise in a hierarchical fashion. The predictable position and growth of secondary loops is pre-patterned and determines adult intestinal topography. We hypothesize based on published accounts that malrotations result from stunted development of secondary loops.

QCD phase diagram using PNJL model with eight-quark interactions

NASA Astrophysics Data System (ADS)

Deb, Paramita; Bhattacharyya, Abhijit; Ghosh, Sanjay K.; Ray, Rajarshi; Lahiri, Anirban

2011-07-01

We present the phase diagram and the fluctuations of different conserved charges like quark number, charge and strangeness at vanishing chemical potential for the 2+1 flavor Polyakov Loop extended Nambu-Jona-Lasinio model with eight-quark interaction terms using three-momentum cutoff regularisation. The main effect of the higher order interaction term is to shift the critical end point to the lower value of the chemical potential and higher value of the temperature. The fluctuations show good qualitative agreement with the lattice data.

NON-POTENTIAL FIELDS IN THE QUIET SUN NETWORK: EXTREME-ULTRAVIOLET AND MAGNETIC FOOTPOINT OBSERVATIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chesny, D. L.; Oluseyi, H. M.; Orange, N. B.

The quiet Sun (QS) magnetic network is known to contain dynamics which are indicative of non-potential fields. Non-potential magnetic fields forming ''S-shaped'' loop arcades can lead to the breakdown of static activity and have only been observed in high temperature X-ray coronal structures—some of which show eruptive behavior. Thus, analysis of this type of atmospheric structuring has been restricted to large-scale coronal fields. Here we provide the first identification of non-potential loop arcades exclusive to the QS supergranulation network. High-resolution Atmospheric Imaging Assembly data from the Solar Dynamics Observatory have allowed for the first observations of fine-scale ''S-shaped'' loop arcadesmore » spanning the network. We have investigated the magnetic footpoint flux evolution of these arcades from Heliospheric and Magnetic Imager data and find evidence of evolving footpoint flux imbalances accompanying the formation of these non-potential fields. The existence of such non-potentiality confirms that magnetic field dynamics leading to the build up of helicity exist at small scales. QS non-potentiality also suggests a self-similar formation process between the QS network and high temperature corona and the existence of self-organized criticality (SOC) in the form of loop-pair reconnection and helicity dissipation. We argue that this type of behavior could lead to eruptive forms of SOC as seen in active region (AR) and X-ray sigmoids if sufficient free magnetic energy is available. QS magnetic network dynamics may be considered as a coronal proxy at supergranular scales, and events confined to the network can even mimic those in coronal ARs.« less

Strong Coupling Gauge Theories in LHC ERA

NASA Astrophysics Data System (ADS)

Fukaya, H.; Harada, M.; Tanabashi, M.; Yamawaki, K.

2011-01-01

AdS/QCD, light-front holography, and the nonperturbative running coupling / Stanley J. Brodsky, Guy de Teramond and Alexandre Deur -- New results on non-abelian vortices - Further insights into monopole, vortex and confinement / K. Konishi -- Study on exotic hadrons at B-factories / Toru Iijima -- Cold compressed baryonic matter with hidden local symmetry and holography / Mannque Rho -- Aspects of baryons in holographic QCD / T. Sakai -- Nuclear force from string theory / K. Hashimoto -- Integrating out holographic QCD back to hidden local symmetry / Masayasu Harada, Shinya Matsuzaki and Koichi Yamawaki -- Holographic heavy quarks and the giant Polyakov loop / Gianluca Grignani, Joanna Karczmarek and Gordon W. Semenoff -- Effect of vector-axial-vector mixing to dilepton spectrum in hot and/or dense matter / Masayasu Harada and Chihiro Sasaki -- Infrared behavior of ghost and gluon propagators compatible with color confinement in Yang-Mills theory with the Gribov horizon / Kei-Ichi Kondo -- Chiral symmetry breaking on the lattice / Hidenori Fukaya [for JLQCD and TWQCD collaborations] -- Gauge-Higgs unification: Stable Higgs bosons as cold dark matter / Yutaka Hosotani -- The limits of custodial symmetry / R. Sekhar Chivukula ... [et al.] -- Higgs searches at the tevatron / Kazuhiro Yamamoto [for the CDF and D[symbol] collaborations] -- The top triangle moose / R. S. Chivukula ... [et al.] -- Conformal phase transition in QCD like theories and beyond / V. A. Miransky -- Gauge-Higgs unification at LHC / Nobuhito Maru and Nobuchika Okada -- W[symbol]W[symbol] scattering in Higgsless models: Identifying better effective theories / Alexander S. Belyaev ... [et al.] -- Holographic estimate of Muon g - 2 / Deog Ki Hong -- Gauge-Higgs dark matter / T. Yamashita -- Topological and curvature effects in a multi-fermion interaction model / T. Inagaki and M. Hayashi -- A model of soft mass generation / J. Hosek -- TeV physics and conformality / Thomas Appelquist -- Conformal Higgs, or techni-dilaton - composite Higgs near conformality / Koichi Yamawaki -- Phase diagram of strongly interacting theories / Francesco Sannino -- Resizing conformal windows / O. Antipin and K. Tuominen -- Nearly conformal gauge theories on the lattice / Zoltan Fodor ... [et al.] -- Going beyond QCD in lattice gauge theory / G. T. Fleming -- Phases of QCD from small to large N[symbol]: (some) lattice results / A. Deuzeman, E. Pallante and M. P. Lombardo -- Lattice gauge theory and (quasi)-conformal technicolor / D. K. Sinclair and J. B. Kogut -- Study of the running coupling constant in 10-flavor QCD with the Schrodinger functional method / N. Yamada ... [et al.] -- Study of the running coupling in twisted Polyakov scheme / T. Aoyama ... [et al.].Running coupling in strong gauge theories via the lattice / Zoltan Fodor ... [et al.] -- Higgsinoless supersymmetry and hidden gravity / Michael L. Graesser, Ryuichiro Kitano and Masafumi Kurachi -- The latest status of LHC and the EWSB physics / S. Asai -- Continuum superpartners from supersymmetric unparticles / Hsin-Chia Cheng -- Review of minimal flavor constraints for technicolor / Hidenori S. Fukano and Francesco Sannino -- Standard model and high energy Lorentz violation / Damiano Anselmi -- Dynamical electroweak symmetry breaking and fourth family / Michio Hashimoto -- Holmorphic supersymmetric Nambu-Jona-Lasino model and dynamical electroweak symmetry breaking / Dong-Won Jung, Otto C. W. Kong and Jae Sik Lee -- Ratchet model of Baryogenesis / Tatsu Takeuchi, Azusa Minamizaki and Akio Sugamoto -- Classical solutions of field equations in Einstein Gauss-Bonnet gravity / P. Suranyi, C. Vaz and L. C. R. Wijewardhana -- Black holes constitute all dark matter / Paul H. Frampton -- Electroweak precision test and Z [symbol] in the three site Higgsless model / Tomohiro Abe -- Chiral symmetry and BRST symmetry breaking, quaternion reality and the lattice simulation / Sadataka Furui -- Holographic techni-dilaton, or conformal Higgs / Kazumoto Haba, Shinya Matsuzaki and Koichi Yamawaki -- Phase structure of topologically massive gauge theory with fermion / Yuichi Hoshino -- New regularization in extra dimensional model and renormalization group flow of the cosmological constant / Shoichi Ichinose -- Spectral analysis of dense two-color QCD / T. Kanazawa, T. Wettig and N. Yamamoto -- NJL model with dimensional regularization at finite temperature / T. Fujihara ... [et al.] -- A new method of evaluating the dynamical chiral symmetry breaking scale and the chiral restoration temperature in general gauge theories by using the non-perturbative renormalization group analyses with general 4-Fermi effective interaction space / Ken-Ichi Aoki, Daisuke Sato and Kazuhiro Miyashita -- The effective chiral Lagrangian with vector mesons and hadronic [symbol] decays / D. Kimura ... [et al.] -- Spontaneous SUSY breaking with anomalous U(1) symmetry in metastable vacua and moduli stabilization / Hiroyuki Nishino -- A new description of the lattice Yang-Mills theory and non-abelian magnetic monopole dominance in the string tension / Akihiro Shibata -- Thermodynamics with unbroken center symmetry in two-flavor QCD / S. Takemoto, M. Harada and C. Sasaki -- Masses of vector bosons in two-color QCD based on the hidden local symmetry / T. Yamaoka, M. Harada and C. Nonaka -- Walking dynamics from string duals / Maurizio Piai -- The quark mass dependence of the nucleon mass in AdS/QCD / Hyo Chul Ahn -- Structure of thermal quasi-fermion in QED/QCD from the Dyson-Schwinger equation / Hisao Nakkagawa -- Critical behaviors of sigma-mode and pion in holographic superconductors / Cheonsoo Park.

Renormalization constants for 2-twist operators in twisted mass QCD

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alexandrou, C.; Computation-based Science and Technology Research Center, The Cyprus Institute, 15 Kypranoros Str., 1645 Nicosia; Constantinou, M.

2011-01-01

Perturbative and nonperturbative results on the renormalization constants of the fermion field and the twist-2 fermion bilinears are presented with emphasis on the nonperturbative evaluation of the one-derivative twist-2 vector and axial-vector operators. Nonperturbative results are obtained using the twisted mass Wilson fermion formulation employing two degenerate dynamical quarks and the tree-level Symanzik improved gluon action. The simulations have been performed for pion masses in the range of about 450-260 MeV and at three values of the lattice spacing a corresponding to {beta}=3.9, 4.05, 4.20. Subtraction of O(a{sup 2}) terms is carried out by performing the perturbative evaluation of thesemore » operators at 1-loop and up to O(a{sup 2}). The renormalization conditions are defined in the RI{sup '}-MOM scheme, for both perturbative and nonperturbative results. The renormalization factors, obtained for different values of the renormalization scale, are evolved perturbatively to a reference scale set by the inverse of the lattice spacing. In addition, they are translated to MS at 2 GeV using 3-loop perturbative results for the conversion factors.« less

QCD inequalities for the nucleon mass and the free energy of baryonic matter.

PubMed

Cohen, Thomas D

2003-07-18

The positivity of the integrand of certain Euclidean space functional integrals for two flavor QCD with degenerate quark masses implies that the free energy per unit volume for QCD with a baryon chemical potential mu(B) (and zero isospin chemical potential) is greater than the free energy with an isospin chemical potential mu(I)=(2 mu(B)/N(c)) (and zero baryon chemical potential). The same result applies to QCD with any number of heavy flavors in addition to the two light flavors so long as the chemical potential is understood as applying to the light quark contributions to the baryon number. This relation implies a bound on the nucleon mass: there exists a particle X in QCD (presumably the pion) such that M(N)> or =(N(c) m(X)/2 I(X)) where m(X) is the mass of the particle and I(X) is its isospin.

The Light-Front Schrödinger Equation and Determination of the Perturbative QCD Scale from Color Confinement

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brodsky, Stanley J.; de Teramond, Guy F.; Deur, Alexandre P.

2015-09-01

The valence Fock-state wavefunctions of the light-front QCD Hamiltonian satisfy a relativistic equation of motion with an effective confining potential U which systematically incorporates the effects of higher quark and gluon Fock states. If one requires that the effective action which underlies the QCD Lagrangian remains conformally invariant and extends the formalism of de Alfaro, Fubini and Furlan to light front Hamiltonian theory, the potential U has a unique form of a harmonic oscillator potential, and a mass gap arises. The result is a nonperturbative relativistic light-front quantum mechanical wave equation which incorporates color confinement and other essential spectroscopic andmore » dynamical features of hadron physics, including a massless pion for zero quark mass and linear Regge trajectories with the same slope in the radial quantum number n and orbital angular momentum L. Only one mass parameter κ appears. Light-front holography thus provides a precise relation between the bound-state amplitudes in the fifth dimension of AdS space and the boost-invariant light-front wavefunctions describing the internal structure of hadrons in physical space-time. We also show how the mass scale κ underlying confinement and hadron masses determines the scale Λ {ovr MS} controlling the evolution of the perturbative QCD coupling. The relation between scales is obtained by matching the nonperturbative dynamics, as described by an effective conformal theory mapped to the light-front and its embedding in AdS space, to the perturbative QCD regime computed to four-loop order. The result is an effective coupling defined at all momenta. The predicted value Λ {ovr MS}=0.328±0.034 GeV is in agreement with the world average 0.339±0.010 GeV. The analysis applies to any renormalization scheme.« less

Actin Hydrophobic Loop (262-274) and Filament Nucleation and Elongation

PubMed Central

Shvetsov, Alexander; Galkin, Vitold E.; Orlova, Albina; Phillips, Martin; Bergeron, Sarah E.; Rubenstein, Peter A.; Egelman, Edward H.; Reisler, Emil

2014-01-01

Summary The importance of actin hydrophobic loop 262-274 dynamics to actin polymerization and filament stability has been shown recently using a yeast actin mutant, L180C/L269C/C374A, in which the hydrophobic loop could be locked in a “parked” conformation by a disulfide bond between C180 and C269. Such a cross-linked G-actin does not form filaments, suggesting nucleation and/or elongation inhibition. To determine the role of loop dynamics in filament nucleation and/or elongation, we studied the polymerization of the cross-linked actin in the presence of cofilin - to assist with actin nucleation - and with phalloidin, to stabilize the elongating filament segments. We demonstrate here that together, but not alone, phalloidin and cofilin co-rescue the polymerization of cross-linked actin. The polymerization was also rescued by filament seeds added together with phalloidin but not with cofilin. Thus, loop immobilization via cross-linking inhibits both filament nucleation and elongation. Nevertheless, the conformational changes needed to catalyze ATP hydrolysis by actin occur in the cross-linked actin. When actin filaments are fully decorated by cofilin the helical twist of F-actin changes by ~ 5° per subunit. Electron microscopic analysis of filaments rescued by cofilin and phalloidin revealed a dense contact between opposite strands in F-actin, and a change of twist by ~ 1° per subunit, indicating either partial or disordered attachment of cofilin to F-actin and/or a competition between cofilin and phalloidin to alter F-actin symmetry. Our findings show an importance of the hydrophobic loop conformational dynamics to both actin nucleation and elongation and reveal that the inhibition of these two steps in the cross-linked actin can be relieved by appropriate factors. PMID:18037437

Investigation of RNA Hairpin Loop Folding with Time-Resolved Infrared Spectroscopy

NASA Astrophysics Data System (ADS)

Stancik, Aaron Lee

Ribonucleic acids (RNAs) are a group of functional biopolymers central to the molecular underpinnings of life. To complete the many processes they mediate, RNAs must fold into precise three-dimensional structures. Hairpin loops are the most ubiquitous and basic structural elements present in all folded RNAs, and are the foundation upon which all complex tertiary structures are built. A hairpin loop forms when a single stranded RNA molecule folds back on itself creating a helical stem of paired bases capped by a loop. This work investigates the formation of UNCG hairpin loops with the sequence 5'-GC(UNCG)GC-3' (N = A, U, G, or C) using both equilibrium infrared (IR) and time-resolved IR spectroscopy. Equilibrium IR melting data were used to determine thermodynamic parameters. Melting temperatures ranged from 50 to 60°C, and enthalpies of unfolding were on the order of 100 kJ/mol. In the time-resolved work, temperature jumps of up to 20°C at 2.5°C increments were obtained with transient relaxation kinetics spanning nanoseconds to hundreds of microseconds. The relaxation kinetics for all of the oligomers studied were fit to first or second order exponentials. Multiple vibrational transitions were probed on each oligomer for fully folded and partially denatured structures. In the time-resolved limit, in contrast to equilibrium melting, RNA does not fold according to two-state behavior. These results are some of the first to show that RNA hairpins fold according to a rugged energy landscape, which contradicts their relatively simple nature. In addition, this work has proven that time-resolved IR spectroscopy is a powerful and novel tool for investigating the earliest events of RNA folding, the formation of the hairpin loop.

Parton distributions and lattice QCD calculations: A community white paper

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Huey-Wen; Nocera, Emanuele R.; Olness, Fred

In the framework of quantum chromodynamics (QCD), parton distribution functions (PDFs) quantify how the momentum and spin of a hadron are divided among its quark and gluon constituents. Two main approaches exist to determine PDFs. The first approach, based on QCD factorization theorems, realizes a QCD analysis of a suitable set of hard-scattering measurements, often using a variety of hadronic observables. The second approach, based on first-principle operator definitions of PDFs, uses lattice QCD to compute directly some PDF-related quantities, such as their moments. Motivated by recent progress in both approaches, in this paper we present an overview of lattice-QCDmore » and global-analysis techniques used to determine unpolarized and polarized proton PDFs and their moments. We provide benchmark numbers to validate present and future lattice-QCD calculations and we illustrate how they could be used to reduce the PDF uncertainties in current unpolarized and polarized global analyses. Finally, this document represents a first step towards establishing a common language between the two communities, to foster dialogue and to further improve our knowledge of PDFs.« less

Parton distributions and lattice QCD calculations: A community white paper

DOE PAGES

Lin, Huey-Wen; Nocera, Emanuele R.; Olness, Fred; ...

2018-01-31

In the framework of quantum chromodynamics (QCD), parton distribution functions (PDFs) quantify how the momentum and spin of a hadron are divided among its quark and gluon constituents. Two main approaches exist to determine PDFs. The first approach, based on QCD factorization theorems, realizes a QCD analysis of a suitable set of hard-scattering measurements, often using a variety of hadronic observables. The second approach, based on first-principle operator definitions of PDFs, uses lattice QCD to compute directly some PDF-related quantities, such as their moments. Motivated by recent progress in both approaches, in this paper we present an overview of lattice-QCDmore » and global-analysis techniques used to determine unpolarized and polarized proton PDFs and their moments. We provide benchmark numbers to validate present and future lattice-QCD calculations and we illustrate how they could be used to reduce the PDF uncertainties in current unpolarized and polarized global analyses. Finally, this document represents a first step towards establishing a common language between the two communities, to foster dialogue and to further improve our knowledge of PDFs.« less

Role of a continuous MHD dynamo in the formation of 3D equilibria in fusion plasmas

NASA Astrophysics Data System (ADS)

Piovesan, P.; Bonfiglio, D.; Cianciosa, M.; Luce, T. C.; Taylor, N. Z.; Terranova, D.; Turco, F.; Wilcox, R. S.; Wingen, A.; Cappello, S.; Chrystal, C.; Escande, D. F.; Holcomb, C. T.; Marrelli, L.; Paz-Soldan, C.; Piron, L.; Predebon, I.; Zaniol, B.; DIII-D, The; RFX-Mod Teams

2017-07-01

Stationary 3D equilibria can form in fusion plasmas via saturation of magnetohydrodynamic (MHD) instabilities or stimulated by external 3D fields. In these cases the current profile is anomalously broad due to magnetic flux pumping produced by the MHD modes. Flux pumping plays an important role in hybrid tokamak plasmas, maintaining the minimum safety factor above unity and thus removing sawteeth. It also enables steady-state hybrid operation, by redistributing non-inductive current driven near the center by electron cyclotron waves. A validated flux pumping model is not yet available, but it would be necessary to extrapolate hybrid operation to future devices. In this work flux pumping physics is investigated for helical core equilibria stimulated by external 3D fields in DIII-D hybrid plasmas. We show that flux pumping can be produced in a continuous way by an MHD dynamo emf. The same effect maintains helical equilibria in reversed-field pinch (RFP) plasmas. The effective MHD dynamo loop voltage is calculated for experimental 3D equilibrium reconstructions, by balancing Ohm’s law over helical flux surfaces, and is consistent with the expected current redistribution. Similar results are also obtained with more sophisticated nonlinear MHD simulations. The same modelling approach is applied to helical RFP states forming spontaneously in RFX-mod as the plasma current is raised above 0.8-1 MA. This comparison allows to identify the underlying physics common to tokamak and RFP: a helical core displacement modulates parallel current density along flux tubes, which requires a helical electrostatic potential to build up, giving rise to a helical MHD dynamo flow.

Common and divergent structural features of a series of corticotropin releasing factor-related peptides.

PubMed

Grace, Christy Rani R; Perrin, Marilyn H; Cantle, Jeffrey P; Vale, Wylie W; Rivier, Jean E; Riek, Roland

2007-12-26

Members of the corticoliberin family include the corticotropin releasing factors (CRFs), sauvagine, the urotensins, and urocortin 1 (Ucn1), which bind to both the CRF receptors CRF-R1 and CRF-R2, and the urocortins 2 (Ucn2) and 3 (Ucn3), which are selective agonists of CRF-R2. Structure activity relationship studies led to several potent and long-acting analogues with selective binding to either one of the receptors. NMR structures of six ligands of this family (the antagonists astressin B and astressin2-B, the agonists stressin1, and the natural ligands human Ucn1, Ucn2, and Ucn3) were determined in DMSO. These six peptides show differences in binding affinities, receptor-selectivity, and NMR structure. Overall, their backbones are alpha-helical, with a small kink or a turn around residues 25-27, resulting in a helix-loop-helix motif. The C-terminal helices are of amphipathic nature, whereas the N-terminal helices vary in their amphipathicity. The C-terminal helices thereby assume a conformation very similar to that of astressin bound to the ECD1 of CRF-R2 recently reported by our group.1 On the basis of an analysis of the observed 3D structures and relative potencies of [Ala]-substituted analogues, it is proposed that both helices could play a crucial role in receptor binding and selectivity. In conclusion, the C-terminal helices may interact along their hydrophobic faces with the ECD1, whereas the entire N-terminal helical surface may be involved in receptor activation. On the basis of the common and divergent features observed in the 3D structures of these ligands, multiple binding models are proposed that may explain their plurality of actions.

Role of a continuous MHD dynamo in the formation of 3D equilibria in fusion plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Piovesan, P.; Bonfiglio, D.; Cianciosa, M.

Stationary 3D equilibria can form in fusion plasmas via saturation of magnetohydrodynamic (MHD) instabilities or stimulated by external 3D fields. In these cases the current profile is anomalously broad due to magnetic flux pumping produced by the MHD modes. Flux pumping plays an important role in hybrid tokamak plasmas, maintaining the minimum safety factor above unity and thus removing sawteeth. It also enables steady-state hybrid operation, by redistributing non-inductive current driven near the center by electron cyclotron waves. A validated flux pumping model is not yet available, but it would be necessary to extrapolate hybrid operation to future devices. Inmore » this work flux pumping physics is investigated for helical core equilibria stimulated by external 3D fields in DIII-D hybrid plasmas. We show that flux pumping can be produced in a continuous way by an MHD dynamo emf. The same effect maintains helical equilibria in reversed-field pinch (RFP) plasmas. The effective MHD dynamo loop voltage is calculated for experimental 3D equilibrium reconstructions, by balancing Ohm’s law over helical flux surfaces, and is consistent with the expected current redistribution. Similar results are also obtained with more sophisticated nonlinear MHD simulations. The same modelling approach is applied to helical RFP states forming spontaneously in RFX-mod as the plasma current is raised above 0.8–1 MA. This comparison allows to identify the underlying physics common to tokamak and RFP: a helical core displacement modulates parallel current density along flux tubes, which requires a helical electrostatic potential to build up, giving rise to a helical MHD dynamo flow.« less

Role of a continuous MHD dynamo in the formation of 3D equilibria in fusion plasmas

DOE PAGES

Piovesan, P.; Bonfiglio, D.; Cianciosa, M.; ...

2017-04-28

Stationary 3D equilibria can form in fusion plasmas via saturation of magnetohydrodynamic (MHD) instabilities or stimulated by external 3D fields. In these cases the current profile is anomalously broad due to magnetic flux pumping produced by the MHD modes. Flux pumping plays an important role in hybrid tokamak plasmas, maintaining the minimum safety factor above unity and thus removing sawteeth. It also enables steady-state hybrid operation, by redistributing non-inductive current driven near the center by electron cyclotron waves. A validated flux pumping model is not yet available, but it would be necessary to extrapolate hybrid operation to future devices. Inmore » this work flux pumping physics is investigated for helical core equilibria stimulated by external 3D fields in DIII-D hybrid plasmas. We show that flux pumping can be produced in a continuous way by an MHD dynamo emf. The same effect maintains helical equilibria in reversed-field pinch (RFP) plasmas. The effective MHD dynamo loop voltage is calculated for experimental 3D equilibrium reconstructions, by balancing Ohm’s law over helical flux surfaces, and is consistent with the expected current redistribution. Similar results are also obtained with more sophisticated nonlinear MHD simulations. The same modelling approach is applied to helical RFP states forming spontaneously in RFX-mod as the plasma current is raised above 0.8–1 MA. This comparison allows to identify the underlying physics common to tokamak and RFP: a helical core displacement modulates parallel current density along flux tubes, which requires a helical electrostatic potential to build up, giving rise to a helical MHD dynamo flow.« less

Crystal structure of the avilamycin resistance-conferring methyltransferase AviRa from Streptomyces viridochromogenes.

PubMed

Mosbacher, Tanja G; Bechthold, Andreas; Schulz, Georg E

2003-05-23

The emergence of antibiotic-resistant bacterial strains is a widespread problem in contemporary medical practice and drug design. It is therefore important to elucidate the underlying mechanism in each case. The methyltransferase AviRa from Streptomyces viridochromogenes mediates resistance to the antibiotic avilamycin, which is closely related to evernimicin, an oligosaccharide antibiotic that has been used in medical studies. The structure of AviRa was determined by X-ray diffraction at 1.5A resolution. Phases were obtained from one selenomethionine residue introduced by site-directed mutagenesis. The chain-fold is similar to that of most methyltransferases, although AviRa contains two additional helices as a specific feature. A putative-binding site for the cofactor S-adenosyl-L-methionine was derived from homologous structures. It agrees with the conserved pattern of interacting amino acid residues. AviRa methylates a specific guanine base within the peptidyltransferase loop of the 23S ribosomal RNA. Guided by the target, the enzyme was docked to the cognate ribosomal surface, where it fit well into a deep cleft without contacting any ribosomal protein. The two additional alpha-helices of AviRa filled a depression in the surface. Since the transferred methyl group of the cofactor is in a pocket beneath the enzyme surface, the targeted guanine base has to flip out for methylation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ayala, Alejandro; Hentschinski, Martin; Jalilian-Marian, Jamal

Azimuthal angular correlations between produced hadrons/jets in high energy collisions are a sensitive probe of the dynamics of QCD at small x. Here we derive the triple differential cross section for inclusive production of 3 polarized partons in DIS at small x using the spinor helicity formalism. The target proton or nucleus is described using the Color Glass Condensate (CGC) formalism. The resulting expressions are used to study azimuthal angular correlations between produced partons in order to probe the gluon structure of the target hadron or nucleus. Finally, our analytic expressions can also be used to calculate the real partmore » of the Next to Leading Order (NLO) corrections to di-hadron production in DIS by integrating out one of the three final state partons.« less

Electroexcitation of nucleon resonances from CLAS data on single pion electroproduction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aznauryan, I. G.; Yerevan Physics Institute, 375036 Yerevan; Burkert, V. D.

2009-11-15

We present results on the electroexcitation of the low mass resonances {delta}(1232)P{sub 33}, N(1440)P{sub 11}, N(1520)D{sub 13}, and N(1535)S{sub 11} in a wide range of Q{sup 2}. The results were obtained in the comprehensive analysis of data from the Continuous Electron Beam Accelerator Facility (CEBAF) large acceptance spectrometer (CLAS) detector at the Thomas Jefferson National Accelerator Facility (JLab) on differential cross sections, longitudinally polarized beam asymmetries, and longitudinal target and beam-target asymmetries for {pi} electroproduction off the proton. The data were analyzed using two conceptually different approaches--fixed-t dispersion relations and a unitary isobar model--allowing us to draw conclusions on themore » model sensitivity of the obtained electrocoupling amplitudes. The amplitudes for the {delta}(1232)P{sub 33} show the importance of a meson-cloud contribution to quantitatively explain the magnetic dipole strength, as well as the electric and scalar quadrupole transitions. They do not show any tendency of approaching the pQCD regime for Q{sup 2}{<=}6 GeV{sup 2}. For the Roper resonance, N(1440)P{sub 11}, the data provide strong evidence that this state is a predominantly radial excitation of a three-quark (3q) ground state. Measured in pion electroproduction, the transverse helicity amplitude for the N(1535)S{sub 11} allowed us to obtain the branching ratios of this state to the {pi}N and {eta}N channels via comparison with the results extracted from {eta} electroproduction. The extensive CLAS data also enabled the extraction of the {gamma}*p{yields}N(1520)D{sub 13} and N(1535)S{sub 11} longitudinal helicity amplitudes with good precision. For the N(1535)S{sub 11}, these results became a challenge for quark models and may be indicative of large meson-cloud contributions or of representations of this state that differ from a 3q excitation. The transverse amplitudes for the N(1520)D{sub 13} clearly show the rapid changeover from helicity-3/2 dominance at the real photon point to helicity-1/2 dominance at Q{sup 2}>1 GeV{sup 2}, confirming a long-standing prediction of the constituent quark model.« less

A generalized analysis of hydrophobic and loop clusters within globular protein sequences

PubMed Central

Eudes, Richard; Le Tuan, Khanh; Delettré, Jean; Mornon, Jean-Paul; Callebaut, Isabelle

2007-01-01

Background Hydrophobic Cluster Analysis (HCA) is an efficient way to compare highly divergent sequences through the implicit secondary structure information directly derived from hydrophobic clusters. However, its efficiency and application are currently limited by the need of user expertise. In order to help the analysis of HCA plots, we report here the structural preferences of hydrophobic cluster species, which are frequently encountered in globular domains of proteins. These species are characterized only by their hydrophobic/non-hydrophobic dichotomy. This analysis has been extended to loop-forming clusters, using an appropriate loop alphabet. Results The structural behavior of hydrophobic cluster species, which are typical of protein globular domains, was investigated within banks of experimental structures, considered at different levels of sequence redundancy. The 294 more frequent hydrophobic cluster species were analyzed with regard to their association with the different secondary structures (frequencies of association with secondary structures and secondary structure propensities). Hydrophobic cluster species are predominantly associated with regular secondary structures, and a large part (60 %) reveals preferences for α-helices or β-strands. Moreover, the analysis of the hydrophobic cluster amino acid composition generally allows for finer prediction of the regular secondary structure associated with the considered cluster within a cluster species. We also investigated the behavior of loop forming clusters, using a "PGDNS" alphabet. These loop clusters do not overlap with hydrophobic clusters and are highly associated with coils. Finally, the structural information contained in the hydrophobic structural words, as deduced from experimental structures, was compared to the PSI-PRED predictions, revealing that β-strands and especially α-helices are generally over-predicted within the limits of typical β and α hydrophobic clusters. Conclusion The dictionary of hydrophobic clusters described here can help the HCA user to interpret and compare the HCA plots of globular protein sequences, as well as provides an original fundamental insight into the structural bricks of protein folds. Moreover, the novel loop cluster analysis brings additional information for secondary structure prediction on the whole sequence through a generalized cluster analysis (GCA), and not only on regular secondary structures. Such information lays the foundations for developing a new and original tool for secondary structure prediction. PMID:17210072

Mellin-Barnes approach to hadronic vacuum polarization and gμ-2

NASA Astrophysics Data System (ADS)

Charles, Jérôme; de Rafael, Eduardo; Greynat, David

2018-04-01

It is shown that with a precise determination of a few derivatives of the hadronic vacuum polarization (HVP) self-energy function Π (Q2) at Q2=0 , from lattice QCD (LQCD) or from a dedicated low-energy experiment, one can obtain an evaluation of the lowest order HVP contribution to the anomalous magnetic moment of the muon aμHVP with an accuracy comparable to the one reached using the e+e- annihilation cross section into hadrons. The technique of Mellin-Barnes approximants (MBa) that we propose is illustrated in detail with the example of the two loop vacuum polarization function in QED. We then apply it to the first few moments of the hadronic spectral function obtained from experiment and show that the resulting MBa evaluations of aμHVP converge very quickly to the full experimental determination.

Higgs Boson Pair Production in Gluon Fusion at Next-to-Leading Order with Full Top-Quark Mass Dependence.

PubMed

Borowka, S; Greiner, N; Heinrich, G; Jones, S P; Kerner, M; Schlenk, J; Schubert, U; Zirke, T

2016-07-01

We present the calculation of the cross section and invariant mass distribution for Higgs boson pair production in gluon fusion at next-to-leading order (NLO) in QCD. Top-quark masses are fully taken into account throughout the calculation. The virtual two-loop amplitude has been generated using an extension of the program GoSam supplemented with an interface to Reduze for the integral reduction. The occurring integrals have been calculated numerically using the program SecDec. Our results, including the full top-quark mass dependence for the first time, allow us to assess the validity of various approximations proposed in the literature, which we also recalculate. We find substantial deviations between the NLO result and the different approximations, which emphasizes the importance of including the full top-quark mass dependence at NLO.

The generalized scheme-independent Crewther relation in QCD

DOE PAGES

Shen, Jian-Ming; Wu, Xing-Gang; Ma, Yang; ...

2017-05-10

The Principle of Maximal Conformality (PMC) provides a systematic way to set the renormalization scales order-by-order for any perturbative QCD calculable processes. The resulting predictions are independent of the choice of renormalization scheme, a requirement of renormalization group invariance. The Crewther relation, which was originally derived as a consequence of conformally invariant field theory, provides a remarkable connection between two observables when the β function vanishes: one can show that the product of the Bjorken sum rule for spin-dependent deep inelastic lepton–nucleon scattering times the Adler function, defined from the cross section for electron–positron annihilation into hadrons, has no pQCD radiative corrections. The “Generalized Crewther Relation” relates these two observables for physical QCD with nonzero β function; specifically, it connects the non-singlet Adler function (D ns) to the Bjorken sum rule coefficient for polarized deep-inelastic electron scattering (C Bjp) at leading twist. A scheme-dependent Δ CSB-term appears in the analysis in order to compensate for the conformal symmetry breaking (CSB) terms from perturbative QCD. In conventional analyses, this normally leads to unphysical dependence in both the choice of the renormalization scheme and the choice of the initial scale at any finite order. However, by applying PMC scale-setting, we can fix the scales of the QCD coupling unambiguously at every order of pQCD. The result is that both D ns and the inverse coefficient Cmore » $$-1\\atop{Bjp}$$ have identical pQCD coefficients, which also exactly match the coefficients of the corresponding conformal theory. Thus one obtains a new generalized Crewther relation for QCD which connects two effective charges, $$\\hat{α}$$ d(Q)=Σ i≥1$$\\hat{α}^i\\atop{g1}$$(Qi), at their respective physical scales. This identity is independent of the choice of the renormalization scheme at any finite order, and the dependence on the choice of the initial scale is negligible. Lastly, similar scale-fixed commensurate scale relations also connect other physical observables at their physical momentum scales, thus providing convention-independent, fundamental precision tests of QCD.« less

The generalized scheme-independent Crewther relation in QCD

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shen, Jian-Ming; Wu, Xing-Gang; Ma, Yang

The Principle of Maximal Conformality (PMC) provides a systematic way to set the renormalization scales order-by-order for any perturbative QCD calculable processes. The resulting predictions are independent of the choice of renormalization scheme, a requirement of renormalization group invariance. The Crewther relation, which was originally derived as a consequence of conformally invariant field theory, provides a remarkable connection between two observables when the β function vanishes: one can show that the product of the Bjorken sum rule for spin-dependent deep inelastic lepton–nucleon scattering times the Adler function, defined from the cross section for electron–positron annihilation into hadrons, has no pQCD radiative corrections. The “Generalized Crewther Relation” relates these two observables for physical QCD with nonzero β function; specifically, it connects the non-singlet Adler function (D ns) to the Bjorken sum rule coefficient for polarized deep-inelastic electron scattering (C Bjp) at leading twist. A scheme-dependent Δ CSB-term appears in the analysis in order to compensate for the conformal symmetry breaking (CSB) terms from perturbative QCD. In conventional analyses, this normally leads to unphysical dependence in both the choice of the renormalization scheme and the choice of the initial scale at any finite order. However, by applying PMC scale-setting, we can fix the scales of the QCD coupling unambiguously at every order of pQCD. The result is that both D ns and the inverse coefficient Cmore » $$-1\\atop{Bjp}$$ have identical pQCD coefficients, which also exactly match the coefficients of the corresponding conformal theory. Thus one obtains a new generalized Crewther relation for QCD which connects two effective charges, $$\\hat{α}$$ d(Q)=Σ i≥1$$\\hat{α}^i\\atop{g1}$$(Qi), at their respective physical scales. This identity is independent of the choice of the renormalization scheme at any finite order, and the dependence on the choice of the initial scale is negligible. Lastly, similar scale-fixed commensurate scale relations also connect other physical observables at their physical momentum scales, thus providing convention-independent, fundamental precision tests of QCD.« less

Vortex multiplication in applied flow: A precursor to superfluid turbulence.

PubMed

Finne, A P; Eltsov, V B; Eska, G; Hänninen, R; Kopu, J; Krusius, M; Thuneberg, E V; Tsubota, M

2006-03-03

A surface-mediated process is identified in 3He-B which generates vortices at a roughly constant rate. It precedes a faster form of turbulence where intervortex interactions dominate. This precursor becomes observable when vortex loops are introduced in low-velocity rotating flow at sufficiently low mutual friction dissipation at temperatures below 0.5Tc. Our measurements indicate that the formation of new loops is associated with a single vortex interacting in the applied flow with the sample boundary. Numerical calculations show that the single-vortex instability arises when a helical Kelvin wave expands from a reconnection kink at the wall and then intersects again with the wall.

Tensor integrand reduction via Laurent expansion

DOE PAGES

Hirschi, Valentin; Peraro, Tiziano

2016-06-09

We introduce a new method for the application of one-loop integrand reduction via the Laurent expansion algorithm, as implemented in the public C++ library Ninja. We show how the coefficients of the Laurent expansion can be computed by suitable contractions of the loop numerator tensor with cut-dependent projectors, making it possible to interface Ninja to any one-loop matrix element generator that can provide the components of this tensor. We implemented this technique in the Ninja library and interfaced it to MadLoop, which is part of the public MadGraph5_aMC@NLO framework. We performed a detailed performance study, comparing against other public reductionmore » tools, namely CutTools, Samurai, IREGI, PJFry++ and Golem95. We find that Ninja out-performs traditional integrand reduction in both speed and numerical stability, the latter being on par with that of the tensor integral reduction tool Golem95 which is however more limited and slower than Ninja. Lastly, we considered many benchmark multi-scale processes of increasing complexity, involving QCD and electro-weak corrections as well as effective non-renormalizable couplings, showing that Ninja’s performance scales well with both the rank and multiplicity of the considered process.« less

Hadronic light-by-light scattering contribution to the muon g - 2 on the lattice

NASA Astrophysics Data System (ADS)

Asmussen, Nils; Gérardin, Antoine; Green, Jeremy; Gryniuk, Oleksii; von Hippel, Georg; Meyer, Harvey B.; Nyffeler, Andreas; Pascalutsa, Vladimir; Wittig, Hartmut

2018-05-01

We briefly review several activities at Mainz related to hadronic light-by-light scattering (HLbL) using lattice QCD. First we present a position-space approach to the HLbL contribution in the muon g̅2, where we focus on exploratory studies of the pion-pole contribution in a simple model and the lepton loop in QED in the continuum and in infinite volume. The second part describes a lattice calculation of the double-virtual pion transition form factor Fπ0γ*γ* (q21; q21) in the spacelike region with photon virtualities up to 1.5 GeV2 which paves the way for a lattice calculation of the pion-pole contribution to HLbL. The third topic involves HLbL forward scattering amplitudes calculated in lattice QCD which can be described, using dispersion relations (HLbL sum rules), by γ*γ* → hadrons fusion cross sections and then compared with phenomenological models.

Bayesian Approach to Spectral Function Reconstruction for Euclidean Quantum Field Theories

NASA Astrophysics Data System (ADS)

Burnier, Yannis; Rothkopf, Alexander

2013-11-01

We present a novel approach to the inference of spectral functions from Euclidean time correlator data that makes close contact with modern Bayesian concepts. Our method differs significantly from the maximum entropy method (MEM). A new set of axioms is postulated for the prior probability, leading to an improved expression, which is devoid of the asymptotically flat directions present in the Shanon-Jaynes entropy. Hyperparameters are integrated out explicitly, liberating us from the Gaussian approximations underlying the evidence approach of the maximum entropy method. We present a realistic test of our method in the context of the nonperturbative extraction of the heavy quark potential. Based on hard-thermal-loop correlator mock data, we establish firm requirements in the number of data points and their accuracy for a successful extraction of the potential from lattice QCD. Finally we reinvestigate quenched lattice QCD correlators from a previous study and provide an improved potential estimation at T=2.33TC.

Bayesian approach to spectral function reconstruction for Euclidean quantum field theories.

PubMed

Burnier, Yannis; Rothkopf, Alexander

2013-11-01

We present a novel approach to the inference of spectral functions from Euclidean time correlator data that makes close contact with modern Bayesian concepts. Our method differs significantly from the maximum entropy method (MEM). A new set of axioms is postulated for the prior probability, leading to an improved expression, which is devoid of the asymptotically flat directions present in the Shanon-Jaynes entropy. Hyperparameters are integrated out explicitly, liberating us from the Gaussian approximations underlying the evidence approach of the maximum entropy method. We present a realistic test of our method in the context of the nonperturbative extraction of the heavy quark potential. Based on hard-thermal-loop correlator mock data, we establish firm requirements in the number of data points and their accuracy for a successful extraction of the potential from lattice QCD. Finally we reinvestigate quenched lattice QCD correlators from a previous study and provide an improved potential estimation at T=2.33T(C).

Spin polarized photons from an axially charged plasma at weak coupling: Complete leading order

DOE PAGES

Mamo, Kiminad A.; Yee, Ho-Ung

2016-03-24

In the presence of (approximately conserved) axial charge in the QCD plasma at finite temperature, the emitted photons are spin aligned, which is a unique P- and CP-odd signature of axial charge in the photon emission observables. We compute this “P-odd photon emission rate” in a weak coupling regime at a high temperature limit to complete leading order in the QCD coupling constant: the leading log as well as the constant under the log. As in the P-even total emission rate in the literature, the computation of the P-odd emission rate at leading order consists of three parts: (1) Comptonmore » and pair annihilation processes with hard momentum exchange, (2) soft t- and u-channel contributions with hard thermal loop resummation, (3) Landau-Pomeranchuk-Migdal resummation of collinear bremsstrahlung and pair annihilation. In conclusion, we present analytical and numerical evaluations of these contributions to our P-odd photon emission rate observable.« less

The effective hyper-Kähler potential in the N = 2 supersymmetric QCD

NASA Astrophysics Data System (ADS)

Ketov, Sergei V.

1997-02-01

The effective low-energy hyper-Kähler potential for a massive N = 2 matter in N = 2 super-QCD is investigated. TheN = 2 extended supersymmetry severely restricts the N = 2 matter self-couplings so that their exact form can be fixed by a few parameters, which is apparent in the N = 2 harmonic superspace. In the N = 2 QED with a single matter hypermultiplet, the one-loop perturbative calculations lead to the Taub-NUT hyper-Kähler metric in the massive case, and a free metric in the massless case. It is remarkable that the naive non-renormalization `theorem' does not apply. There exists a manifestly N = 2 supersymmetric duality transformation converting the low-energy effective action for the N = 2 QED hypermultiplet into a sum of the quadratic and the improved (non-polynomial) actions for an N = 2 tensor multiplet. The duality transformation also gives a simple connection between the low-energy effective action in the N = 2 harmonic superspace and the component results.

Gauge-invariant screening masses and static quark free energies in Nf=2 +1 QCD at nonzero baryon density

NASA Astrophysics Data System (ADS)

Andreoli, Michele; Bonati, Claudio; D'Elia, Massimo; Mesiti, Michele; Negro, Francesco; Rucci, Andrea; Sanfilippo, Francesco

2018-03-01

We discuss the extension of gauge-invariant electric and magnetic screening masses in the quark-gluon plasma to the case of a finite baryon density, defining them in terms of a matrix of Polyakov loop correlators. We present lattice results for Nf=2 +1 QCD with physical quark masses, obtained using the imaginary chemical potential approach, which indicate that the screening masses increase as a function of μB. A separate analysis is carried out for the theoretically interesting case μB/T =3 i π , where charge conjugation is not explicitly broken and the usual definition of the screening masses can be used for temperatures below the Roberge-Weiss transition. Finally, we investigate the dependence of the static quark free energy on the baryon chemical potential, showing that it is a decreasing function of μB, which displays a peculiar behavior as the pseudocritical transition temperature at μB=0 is approached.

Moving heavy quarkonium entropy, effective string tension, and the QCD phase diagram

NASA Astrophysics Data System (ADS)

Chen, Xun; Feng, Sheng-Qin; Shi, Ya-Fei; Zhong, Yang

2018-03-01

The entropy and effective string tension of the moving heavy quark-antiquark pair in the strongly coupled plasmas are calculated by using a deformed an anti-de Sitter/Reissner-Nordström black hole metric. A sharp peak of the heavy-quarkonium entropy around the deconfinement transition can be realized in our model, which is consistent with the lattice QCD result. The effective string tension of the heavy quark-antiquark pair is related to the deconfinement phase transition. Thus, we investigate the deconfinement phase transition by analyzing the characteristics of the effective string tension with different temperatures, chemical potentials, and rapidities. It is found that the results of phase diagram calculated through effective string tension are in agreement with results calculated through a Polyakov loop. We argue that a moving system will reach the phase transition point at a lower temperature and chemical potential than a stationary system. It means that the lifetime of the moving quark-gluon plasma become longer than the static one.

Strange-quark asymmetry in the proton in chiral effective theory

DOE PAGES

Wang, X. G.; Ji, Chueng -Ryong; Melnitchouk, W.; ...

2016-11-29

We perform a comprehensive analysis of the strange-antistrange parton distribution function (PDF) asymmetry in the proton in the framework of chiral effective theory, including the full set of lowest-order kaon loop diagrams with off-shell and contact interactions, in addition to the usual on-shell contributions previously discussed in the literature. We identify the presence of δ-function contributions to the s¯ PDF at x = 0, with a corresponding valencelike component of the s-quark PDF at larger x, which allows greater flexibility for the shape of s–s¯. Expanding the moments of the PDFs in terms of the pseudoscalar kaon mass, we computemore » the leading nonanalytic behavior of the number and momentum integrals of the s and s¯ distributions, consistent with the chiral symmetry of QCD. Lastly, we discuss the implications of our results for the understanding of the NuTeV anomaly and for the phenomenology of strange-quark PDFs in global QCD analysis.« less

Integrated analysis of particle interactions at hadron colliders Report of research activities in 2010-2015

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nadolsky, Pavel M.

2015-08-31

The report summarizes research activities of the project ”Integrated analysis of particle interactions” at Southern Methodist University, funded by 2010 DOE Early Career Research Award DE-SC0003870. The goal of the project is to provide state-of-the-art predictions in quantum chromodynamics in order to achieve objectives of the LHC program for studies of electroweak symmetry breaking and new physics searches. We published 19 journal papers focusing on in-depth studies of proton structure and integration of advanced calculations from different areas of particle phenomenology: multi-loop calculations, accurate long-distance hadronic functions, and precise numerical programs. Methods for factorization of QCD cross sections were advancedmore » in order to develop new generations of CTEQ parton distribution functions (PDFs), CT10 and CT14. These distributions provide the core theoretical input for multi-loop perturbative calculations by LHC experimental collaborations. A novel ”PDF meta-analysis” technique was invented to streamline applications of PDFs in numerous LHC simulations and to combine PDFs from various groups using multivariate stochastic sampling of PDF parameters. The meta-analysis will help to bring the LHC perturbative calculations to the new level of accuracy, while reducing computational efforts. The work on parton distributions was complemented by development of advanced perturbative techniques to predict observables dependent on several momentum scales, including production of massive quarks and transverse momentum resummation at the next-to-next-to-leading order in QCD.« less

Tornado-Like Evolution of A Kink-Unstable Solar Prominence

NASA Astrophysics Data System (ADS)

Wang, W.; Liu, R.; Wang, Y.

2016-12-01

We report on the tornado-like evolution of a quiescent prominence on 2014 November 1. The evolution started with a slow rise of the eastern section of the prominence into an arch-shaped structure as high as 150 Mm above the limb, and then the arch experienced a moderate, left-handed writhing. Following the writhing, the originally dark prominence material became in emission in the Fe IX 171 °A passband, and a braiding structure appeared at the eastern edge of the writhing prominence body, whose unraveling process was associated with a transient brightening in EUV and apparently contributed to the formation of a curtain-like structure (CLS), which consisted of myriads of thread-like loops rotating counterclockwise about the vertical if viewed from above. Material sliding along these loops landed outside of the prominence channel. The tornado was eventually disintegrated and the remaining material flew along a lefthanded helical path of approximately a full turn, as confirmed through stereoscopic reconstruction, into the cavity of the stable, western section of the prominence. We suggest that the tornado-like evolution of the prominence was regulated by the helical kink instability, and that the CLS forms through magnetic reconnections between the flux-rope flux and the overlying flux.

NMR structural study of the intracellular loop 3 of the serotonin 5-HT(1A) receptor and its interaction with calmodulin.

PubMed

Chen, Angela Shuyi; Kim, Young Mee; Gayen, Shovanlal; Huang, Qiwei; Raida, Manfred; Kang, Congbao

2011-09-01

The serotonin (5-HT(1A)) receptor, a G-protein-coupled receptor (GPCR), plays important roles in serotonergic signaling in the central nervous system. The third intracellular loop (ICL3) of the 5-HT(1A) receptor has been shown to be important for the regulation of this receptor through interactions with proteins such as G-proteins and calmodulin. In this study, the ICL3 of 5-HT(1A) receptor was expressed in E. coli and purified. Gel filtration and mass spectrometry were used to confirm the molecular weight of the purified ICL3. Secondary structure analysis using circular dichroism (CD) demonstrated the presence of α-helical structures. Backbone assignment of ICL3 was achieved using three-dimensional experiments. A chemical shift index and Talos+ analysis showed that residues E326 to R339 form α-helical structure. Residues G256 to S269 of ICL3 were shown to be a novel region that has a molecular interaction with calmodulin in titration assays. Peptide derived from the ICL3 containing residues from G256 to S269 also showed molecular interaction with calmodulin. Copyright © 2011 Elsevier B.V. All rights reserved.

Tornado-like Evolution of a Kink-unstable Solar Prominence

NASA Astrophysics Data System (ADS)

Wang, Wensi; Liu, Rui; Wang, Yuming

2017-01-01

We report on the tornado-like evolution of a quiescent prominence on 2014 November 1. The eastern section of the prominence first rose slowly, transforming into an arch-shaped structure as high as ˜150 Mm above the limb; the arch then writhed moderately in a left-handed sense, while the original dark prominence material emitted in the Fe ix 171 Å passband, and a braided structure appeared at the eastern edge of the warped arch. The unraveling of the braided structure was associated with a transient brightening in the EUV and apparently contributed to the formation of a curtain-like structure (CLS). The CLS consisted of myriad thread-like loops rotating counterclockwise about the vertical if viewed from above. Heated prominence material was observed to slide along these loops and land outside the filament channel. The tornado eventually disintegrated and the remaining material flew along a left-handed helical path constituting approximately a full turn, as corroborated through stereoscopic reconstruction, into the cavity of the stable, western section of the prominence. We suggest that the tornado-like evolution of the prominence was governed by the helical kink instability, and that the CLS formed through magnetic reconnections between the prominence field and the overlying coronal field.

ADP/ATP mitochondrial carrier MD simulations to shed light on the structural-dynamical events that, after an additional mutation, restore the function in a pathological single mutant.

PubMed

Di Marino, Daniele; Oteri, Francesco; Morozzo Della Rocca, Blasco; Chillemi, Giovanni; Falconi, Mattia

2010-12-01

Molecular dynamics simulations of the wild type bovine ADP/ATP mitochondrial carrier, and of the single Ala113Pro and double Ala113Pro/Val180Met mutants, embedded in a lipid bilayer, have been carried out for 30ns to shed light on the structural-dynamical changes induced by the Val180Met mutation restoring the carrier function in the Ala113Pro pathologic mutant. Principal component analysis indicates that, for the three systems, the protein dynamics is mainly characterized by the motion of the matrix loops and of the odd-numbered helices having a conserved proline in their central region. Analysis of the motions shows a different behaviour of single pathological mutant with respect of the other two systems. The single mutation induces a regularization and rigidity of the H3 helix, lost upon the introduction of the second mutation. This is directly correlated to the salt bridge distribution involving residues Arg79, Asp134 and Arg234, hypothesized to interact with the substrate. In fact, in the wild type simulation two stable inter-helices salt bridges, crucial for substrate binding, are present almost over all the simulation time. In line with the impaired ADP transport, one salt interaction is lost in the single mutant trajectory but reappears in the double mutant simulation, where a salt bridge network matching the wild type is restored. Other important structural-dynamical properties, such as the trans-membrane helices mobility, analyzed via the principal component analysis, are similar for the wild type and double mutant while are different for the single mutant, providing a mechanistic explanation for their different functional properties. Copyright © 2010 Elsevier Inc. All rights reserved.

In human pseudouridine synthase 1 (hPus1), a C-terminal helical insert blocks tRNA from binding in the same orientation as in the Pus1 bacterial homologue TruA, consistent with their different target selectivities.

PubMed

Czudnochowski, Nadine; Wang, Amy Liya; Finer-Moore, Janet; Stroud, Robert M

2013-10-23

Human pseudouridine (Ψ) synthase Pus1 (hPus1) modifies specific uridine residues in several non-coding RNAs: tRNA, U2 spliceosomal RNA, and steroid receptor activator RNA. We report three structures of the catalytic core domain of hPus1 from two crystal forms, at 1.8Å resolution. The structures are the first of a mammalian Ψ synthase from the set of five Ψ synthase families common to all kingdoms of life. hPus1 adopts a fold similar to bacterial Ψ synthases, with a central antiparallel β-sheet flanked by helices and loops. A flexible hinge at the base of the sheet allows the enzyme to open and close around an electropositive active-site cleft. In one crystal form, a molecule of Mes [2-(N-morpholino)ethane sulfonic acid] mimics the target uridine of an RNA substrate. A positively charged electrostatic surface extends from the active site towards the N-terminus of the catalytic domain, suggesting an extensive binding site specific for target RNAs. Two α-helices C-terminal to the core domain, but unique to hPus1, extend along the back and top of the central β-sheet and form the walls of the RNA binding surface. Docking of tRNA to hPus1 in a productive orientation requires only minor conformational changes to enzyme and tRNA. The docked tRNA is bound by the electropositive surface of the protein employing a completely different binding mode than that seen for the tRNA complex of the Escherichia coli homologue TruA. Copyright © 2013 Elsevier Ltd. All rights reserved.

Crenactin from Pyrobaculum calidifontis is closely related to actin in structure and forms steep helical filaments

PubMed Central

Izoré, Thierry; Duman, Ramona; Kureisaite-Ciziene, Danguole; Löwe, Jan

2014-01-01

Polymerising proteins of the actin family are nearly ubiquitous. Crenactins, restricted to Crenarchaea, are more closely related to actin than bacterial MreB. Crenactins occur in gene clusters hinting at an unknown, but conserved function. We solved the crystal structure of crenactin at 3.2 Å resolution. The protein crystallises as a continuous right-handed helix with 8 subunits per complete turn, spanning 419 Å. The structure of crenactin shows several loops that are longer than in actin, but overall, crenactin is closely related to eukaryotic actin, with an RMSD of 1.6 Å. Crenactin filaments imaged by electron microscopy showed polymers with very similar helical parameters. PMID:24486010

Elucidating Molecular Motion through Structural and Dynamic Filters of Energy-Minimized Conformer Ensembles

PubMed Central

2015-01-01

Complex RNA structures are constructed from helical segments connected by flexible loops that move spontaneously and in response to binding of small molecule ligands and proteins. Understanding the conformational variability of RNA requires the characterization of the coupled time evolution of interconnected flexible domains. To elucidate the collective molecular motions and explore the conformational landscape of the HIV-1 TAR RNA, we describe a new methodology that utilizes energy-minimized structures generated by the program “Fragment Assembly of RNA with Full-Atom Refinement (FARFAR)”. We apply structural filters in the form of experimental residual dipolar couplings (RDCs) to select a subset of discrete energy-minimized conformers and carry out principal component analyses (PCA) to corroborate the choice of the filtered subset. We use this subset of structures to calculate solution T1 and T1ρ relaxation times for 13C spins in multiple residues in different domains of the molecule using two simulation protocols that we previously published. We match the experimental T1 times to within 2% and the T1ρ times to within less than 10% for helical residues. These results introduce a protocol to construct viable dynamic trajectories for RNA molecules that accord well with experimental NMR data and support the notion that the motions of the helical portions of this small RNA can be described by a relatively small number of discrete conformations exchanging over time scales longer than 1 μs. PMID:24479561

The four-loop six-gluon NMHV ratio function

DOE PAGES

Dixon, Lance J.; von Hippel, Matt; McLeod, Andrew J.

2016-01-11

We use the hexagon function bootstrap to compute the ratio function which characterizes the next-to-maximally-helicity-violating (NMHV) six-point amplitude in planar N=4 super-Yang-Mills theory at four loops. A powerful constraint comes from dual superconformal invariance, in the form of a Q¯ differential equation, which heavily constrains the first derivatives of the transcendental functions entering the ratio function. At four loops, it leaves only a 34-parameter space of functions. Constraints from the collinear limits, and from the multi-Regge limit at the leading-logarithmic (LL) and next-to-leading-logarithmic (NLL) order, suffice to fix these parameters and obtain a unique result. We test the result againstmore » multi-Regge predictions at NNLL and N 3LL, and against predictions from the operator product expansion involving one and two flux-tube excitations; all cross-checks are satisfied. We study the analytical and numerical behavior of the parity-even and parity-odd parts on various lines and surfaces traversing the three-dimensional space of cross ratios. As part of this program, we characterize all irreducible hexagon functions through weight eight in terms of their coproduct. As a result, we also provide representations of the ratio function in particular kinematic regions in terms of multiple polylogarithms.« less

The four-loop six-gluon NMHV ratio function

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dixon, Lance J.; von Hippel, Matt; McLeod, Andrew J.

2016-01-11

We use the hexagon function bootstrap to compute the ratio function which characterizes the next-to-maximally-helicity-violating (NMHV) six-point amplitude in planar N = 4 super-Yang-Mills theory at four loops. A powerful constraint comes from dual superconformal invariance, in the form of a Q - differential equation, which heavily constrains the first derivatives of the transcendental functions entering the ratio function. At four loops, it leaves only a 34-parameter space of functions. Constraints from the collinear limits, and from the multi-Regge limit at the leading-logarithmic (LL) and next-to-leading-logarithmic (NLL) order, suffice to fix these parameters and obtain a unique result. We testmore » the result against multi- Regge predictions at NNLL and N 3LL, and against predictions from the operator product expansion involving one and two flux-tube excitations; all cross-checks are satisfied. We also study the analytical and numerical behavior of the parity-even and parity-odd parts on various lines and surfaces traversing the three-dimensional space of cross ratios. As part of this program, we characterize all irreducible hexagon functions through weight eight in terms of their coproduct. Furthermore, we provide representations of the ratio function in particular kinematic regions in terms of multiple polylogarithms.« less

Additional strange hadrons from QCD thermodynamics and strangeness freezeout in heavy ion collisions.

PubMed

Bazavov, A; Ding, H-T; Hegde, P; Kaczmarek, O; Karsch, F; Laermann, E; Maezawa, Y; Mukherjee, Swagato; Ohno, H; Petreczky, P; Schmidt, C; Sharma, S; Soeldner, W; Wagner, M

2014-08-15

We compare lattice QCD results for appropriate combinations of net strangeness fluctuations and their correlations with net baryon number fluctuations with predictions from two hadron resonance gas (HRG) models having different strange hadron content. The conventionally used HRG model based on experimentally established strange hadrons fails to describe the lattice QCD results in the hadronic phase close to the QCD crossover. Supplementing the conventional HRG with additional, experimentally uncharted strange hadrons predicted by quark model calculations and observed in lattice QCD spectrum calculations leads to good descriptions of strange hadron thermodynamics below the QCD crossover. We show that the thermodynamic presence of these additional states gets imprinted in the yields of the ground-state strange hadrons leading to a systematic 5-8 MeV decrease of the chemical freeze-out temperatures of ground-state strange baryons.

Born-Oppenheimer approximation in an effective field theory language

NASA Astrophysics Data System (ADS)

Brambilla, Nora; Krein, Gastão; Tarrús Castellà, Jaume; Vairo, Antonio

2018-01-01

The Born-Oppenheimer approximation is the standard tool for the study of molecular systems. It is founded on the observation that the energy scale of the electron dynamics in a molecule is larger than that of the nuclei. A very similar physical picture can be used to describe QCD states containing heavy quarks as well as light-quarks or gluonic excitations. In this work, we derive the Born-Oppenheimer approximation for QED molecular systems in an effective field theory framework by sequentially integrating out degrees of freedom living at energies above the typical energy scale where the dynamics of the heavy degrees of freedom occurs. In particular, we compute the matching coefficients of the effective field theory for the case of the H2+ diatomic molecule that are relevant to compute its spectrum up to O (m α5). Ultrasoft photon loops contribute at this order, being ultimately responsible for the molecular Lamb shift. In the effective field theory the scaling of all the operators is homogeneous, which facilitates the determination of all the relevant contributions, an observation that may become useful for high-precision calculations. Using the above case as a guidance, we construct under some conditions an effective field theory for QCD states formed by a color-octet heavy quark-antiquark pair bound with a color-octet light-quark pair or excited gluonic state, highlighting the similarities and differences between the QED and QCD systems. Assuming that the multipole expansion is applicable, we construct the heavy-quark potential up to next-to-leading order in the multipole expansion in terms of nonperturbative matching coefficients to be obtained from lattice QCD.

Solution 1H NMR characterization of the axial bonding of the two His in oxidized human cytoglobin

PubMed Central

Bondarenko, Vasyl; Dewilde, Sylvia; Moens, Luc; La Mar, Gerd N.

2008-01-01

Solution 1H NMR spectroscopy has been used to determine the relative strengths (covalency) of the two axial His-Fe bonds in paramagnetic, S = 1/2, human met-cytoglobin. The sequence specific assignments of crucial portions of the proximal and distal helices, together with the magnitude of hyperfine shifts and paramagnetic relaxation, establish that His81 and His113, at the canonical positions E7 and F8 in the myoglobin fold, respectively, are ligated to the iron. The characterized complex (~90%) in solution has protohemin oriented as in crystals, with the remaining ~10% exhibiting the hemin orientation rotated 180° about the α-, γ-meso axis. No evidence could be obtained for any five-coordinate complex (<1%) in equilibrium with the six-coordinate complexes. Extensive sequence-specific assignments on other dipolar shifted helical fragments and loops, together with available alternate crystal coordinates for the complex, allowed the robust determination of the orientation and anisotropies of the paramagnetic susceptibility tensor. The tilt of the major axis is controlled by the His-Fe-His vector, and the rhombic axes by the mean of the imidazole orientations for the two His. The anisotropy of the paramagnetic susceptibility tensor allowed the quantitative factoring of the hyperfine shifts for the two axial His to reveal indistinguishable pattern and magnitudes of the contact shifts or π spin densities, and hence, indistinguishable Fe-imidazole covalency for both Fe-His bonds. PMID:17002396

Ghost-Free APT Analysis of Perturbative QCD Observables

NASA Astrophysics Data System (ADS)

Shirkov, Dmitry V.

The review of the essence and of application of recently devised ghost-free Analytic Perturbation Theory (APT) is presented. First, we discuss the main intrinsic problem of perturbative QCD - ghost singularities and with the resume of its resolving within the APT. By examples for diverse energy and momentum transfer values we show the property of better convergence for the APT modified QCD expansion. It is shown that in the APT analysis the three-loop contribution (sim alpha_s^3) is numerically inessential. This gives raise a hope for practical solution of the well-known problem of non-satisfactory convergence of QFT perturbation series due to its asymptotic nature. Our next result is that a usual perturbative analysis of time-like events is not adequate at sleq 2 GeV2. In particular, this relates to tau decay. Then, for the "high" (f=5) region it is shown that the common NLO, NLLA perturbation approximation widely used there (at 10 GeV lesssimsqrt{s}lesssim 170 GeV) yields a systematic theoretic negative error of a couple per cent level for the bar {alpha}_s^2 values. This results in a conclusion that the bar α_s(M^2_Z) value averaged over the f=5 data appreciably differs < bar {alpha}_s(M^2_Z)rangle_{f=5} simeq 0.124 from the currently popular "world average" (=0.118 ).

Trigger loop dynamics can explain stimulation of intrinsic termination by bacterial RNA polymerase without terminator hairpin contact.

PubMed

Ray-Soni, Ananya; Mooney, Rachel A; Landick, Robert

2017-10-31

In bacteria, intrinsic termination signals cause disassembly of the highly stable elongating transcription complex (EC) over windows of two to three nucleotides after kilobases of RNA synthesis. Intrinsic termination is caused by the formation of a nascent RNA hairpin adjacent to a weak RNA-DNA hybrid within RNA polymerase (RNAP). Although the contributions of RNA and DNA sequences to termination are largely understood, the roles of conformational changes in RNAP are less well described. The polymorphous trigger loop (TL), which folds into the trigger helices to promote nucleotide addition, also is proposed to drive termination by folding into the trigger helices and contacting the terminator hairpin after invasion of the hairpin in the RNAP main cleft [Epshtein V, Cardinale CJ, Ruckenstein AE, Borukhov S, Nudler E (2007) Mol Cell 28:991-1001]. To investigate the contribution of the TL to intrinsic termination, we developed a kinetic assay that distinguishes effects of TL alterations on the rate at which ECs terminate from effects of the TL on the nucleotide addition rate that indirectly affect termination efficiency by altering the time window in which termination can occur. We confirmed that the TL stimulates termination rate, but found that stabilizing either the folded or unfolded TL conformation decreased termination rate. We propose that conformational fluctuations of the TL (TL dynamics), not TL-hairpin contact, aid termination by increasing EC conformational diversity and thus access to favorable termination pathways. We also report that the TL and the TL sequence insertion (SI3) increase overall termination efficiency by stimulating pausing, which increases the flux of ECs into the termination pathway. Published under the PNAS license.

A consensus-guided approach yields a heat-stable alkane-producing enzyme and identifies residues promoting thermostability.

PubMed

Shakeel, Tabinda; Gupta, Mayank; Fatma, Zia; Kumar, Rakesh; Kumar, Raubins; Singh, Rahul; Sharma, Medha; Jade, Dhananjay; Gupta, Dinesh; Fatma, Tasneem; Yazdani, Syed Shams

2018-06-15

Aldehyde-deformylating oxygenase (ADO) is an essential enzyme for production of long-chain alkanes as drop-in biofuels, which are compatible with existing fuel systems. The most active ADOs are present in mesophilic cyanobacteria, especially Nostoc punctiforme Given the potential applications of thermostable enzymes in biorefineries, here we generated a thermostable (Cts)-ADO based on a consensus of ADO sequences from several thermophilic cyanobacterial strains. Using an in silico design pipeline and a metagenome library containing 41 hot-spring microbial communities, we created Cts-ADO. Cts-ADO displayed a 3.8-fold increase in pentadecane production on raising the temperature from 30 to 42 °C, whereas ADO from N. punctiforme (Np-ADO) exhibited a 1.7-fold decline. 3D structure modeling and molecular dynamics simulations of Cts- and Np-ADO at different temperatures revealed differences between the two enzymes in residues clustered on exposed loops of these variants, which affected the conformation of helices involved in forming the ADO catalytic core. In Cts-ADO, this conformational change promoted ligand binding to its preferred iron, Fe2, in the di-iron cluster at higher temperature, but the reverse was observed in Np-ADO. Detailed mapping of residues conferring Cts-ADO thermostability identified four amino acids, which we substituted individually and together in Np-ADO. Among these substitution variants, A161E was remarkably similar to Cts-ADO in terms of activity optima, kinetic parameters, and structure at higher temperature. A161E was located in loop L6, which connects helices H5 and H6, and supported ligand binding to Fe2 at higher temperatures, thereby promoting optimal activity at these temperatures and explaining the increased thermostability of Cts-ADO. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Helicon modes in uniform plasmas. I. Low m modes

NASA Astrophysics Data System (ADS)

Urrutia, J. M.; Stenzel, R. L.

2015-09-01

Helicons are whistler modes with azimuthal wave numbers. They arise in bounded gaseous and solid state plasmas, but the present work shows that very similar modes also exist in unbounded uniform plasmas. The antenna properties determine the mode structure. A simple antenna is a magnetic loop with dipole moment aligned either along or across the ambient background magnetic field B0. For such configurations, the wave magnetic field has been measured in space and time in a large and uniform laboratory plasma. The observed wave topology for a dipole along B0 is similar to that of an m = 0 helicon mode. It consists of a sequence of alternating whistler vortices. For a dipole across B0, an m = 1 mode is excited which can be considered as a transverse vortex which rotates around B0. In m = 0 modes, the field lines are confined to each half-wavelength vortex while for m = 1 modes they pass through the entire wave train. A subset of m = 1 field lines forms two nested helices which rotate in space and time like corkscrews. Depending on the type of the antenna, both m = + 1 and m = -1 modes can be excited. Helicons in unbounded plasmas also propagate transverse to B0. The transverse and parallel wave numbers are about equal and form oblique phase fronts as in whistler Gendrin modes. By superimposing small amplitude fields of several loop antennas, various antenna combinations have been created. These include rotating field antennas, helical antennas, and directional antennas. The radiation efficiency is quantified by the radiation resistance. Since helicons exist in unbounded laboratory plasmas, they can also arise in space plasmas.

Trigger loop dynamics can explain stimulation of intrinsic termination by bacterial RNA polymerase without terminator hairpin contact

PubMed Central

Ray-Soni, Ananya; Mooney, Rachel A.; Landick, Robert

2017-01-01

In bacteria, intrinsic termination signals cause disassembly of the highly stable elongating transcription complex (EC) over windows of two to three nucleotides after kilobases of RNA synthesis. Intrinsic termination is caused by the formation of a nascent RNA hairpin adjacent to a weak RNA−DNA hybrid within RNA polymerase (RNAP). Although the contributions of RNA and DNA sequences to termination are largely understood, the roles of conformational changes in RNAP are less well described. The polymorphous trigger loop (TL), which folds into the trigger helices to promote nucleotide addition, also is proposed to drive termination by folding into the trigger helices and contacting the terminator hairpin after invasion of the hairpin in the RNAP main cleft [Epshtein V, Cardinale CJ, Ruckenstein AE, Borukhov S, Nudler E (2007) Mol Cell 28:991–1001]. To investigate the contribution of the TL to intrinsic termination, we developed a kinetic assay that distinguishes effects of TL alterations on the rate at which ECs terminate from effects of the TL on the nucleotide addition rate that indirectly affect termination efficiency by altering the time window in which termination can occur. We confirmed that the TL stimulates termination rate, but found that stabilizing either the folded or unfolded TL conformation decreased termination rate. We propose that conformational fluctuations of the TL (TL dynamics), not TL-hairpin contact, aid termination by increasing EC conformational diversity and thus access to favorable termination pathways. We also report that the TL and the TL sequence insertion (SI3) increase overall termination efficiency by stimulating pausing, which increases the flux of ECs into the termination pathway. PMID:29078293

The static quark potential from the gauge independent Abelian decomposition

NASA Astrophysics Data System (ADS)

Cundy, Nigel; Cho, Y. M.; Lee, Weonjong; Leem, Jaehoon

2015-06-01

We investigate the relationship between colour confinement and the gauge independent Cho-Duan-Ge Abelian decomposition. The decomposition is defined in terms of a colour field n; the principle novelty of our study is that we have used a unique definition of this field in terms of the eigenvectors of the Wilson Loop. This allows us to establish an equivalence between the path-ordered integral of the non-Abelian gauge fields and an integral over an Abelian restricted gauge field which is tractable both theoretically and numerically in lattice QCD. We circumvent path ordering without requiring an additional path integral. By using Stokes' theorem, we can compute the Wilson Loop in terms of a surface integral over a restricted field strength, and show that the restricted field strength may be dominated by certain structures, which occur when one of the quantities parametrising the colour field n winds itself around a non-analyticity in the colour field. If they exist, these structures will lead to an area law scaling for the Wilson Loop and provide a mechanism for quark confinement. Unlike most studies of confinement using the Abelian decomposition, we do not rely on a dual-Meissner effect to create the inter-quark potential. We search for these structures in quenched lattice QCD. We perform the Abelian decomposition, and compare the electric and magnetic fields with the patterns expected theoretically. We find that the restricted field strength is dominated by objects which may be peaks of a single lattice spacing in size or extended string-like lines of electromagnetic flux. The objects are not isolated monopoles, as they generate electric fields in addition to magnetic fields, and the fields are not spherically symmetric, but may be either caused by a monopole/anti-monopole condensate, some other types of topological objects, or a combination of these. Removing these peaks removes the area law scaling of the string tension, suggesting that they are responsible for confinement.

Symmetry Transition Preserving Chirality in QCD: A Versatile Random Matrix Model

NASA Astrophysics Data System (ADS)

Kanazawa, Takuya; Kieburg, Mario

2018-06-01

We consider a random matrix model which interpolates between the chiral Gaussian unitary ensemble and the Gaussian unitary ensemble while preserving chiral symmetry. This ensemble describes flavor symmetry breaking for staggered fermions in 3D QCD as well as in 4D QCD at high temperature or in 3D QCD at a finite isospin chemical potential. Our model is an Osborn-type two-matrix model which is equivalent to the elliptic ensemble but we consider the singular value statistics rather than the complex eigenvalue statistics. We report on exact results for the partition function and the microscopic level density of the Dirac operator in the ɛ regime of QCD. We compare these analytical results with Monte Carlo simulations of the matrix model.

Fluctuations in the quark-meson model for QCD with isospin chemical potential

NASA Astrophysics Data System (ADS)

Kamikado, Kazuhiko; Strodthoff, Nils; von Smekal, Lorenz; Wambach, Jochen

2013-01-01

We study the two-flavor quark-meson (QM) model with the functional renormalization group (FRG) to describe the effects of collective mesonic fluctuations on the phase diagram of QCD at finite baryon and isospin chemical potentials, μB and μI. With only isospin chemical potential there is a precise equivalence between the competing dynamics of chiral versus pion condensation and that of collective mesonic and baryonic fluctuations in the quark-meson-diquark model for two-color QCD at finite baryon chemical potential. Here, finite μB = 3 μ introduces an additional dimension to the phase diagram as compared to two-color QCD, however. At zero temperature, the (μI, μ) plane of this phase diagram is strongly constrained by the "Silver Blaze problem." In particular, the onset of pion condensation must occur at μI =mπ / 2, independent of μ as long as μ +μI stays below the constituent quark mass of the QM model or the liquid-gas transition line of nuclear matter in QCD. In order to maintain this relation beyond mean field it is crucial to compute the pion mass from its timelike correlator with the FRG in a consistent way.

Spectroscopy -- An introduction and overview

DOE Office of Scientific and Technical Information (OSTI.GOV)

Isgur, N.

1999-02-01

The study of baryons can provide one with critical insights into the nature of QCD in the confinement domain. The key to progress in this field is the identification of its important degrees of freedom. The author explains why he believes that the adiabatic approximation is central to understanding the absence of gluonic excitations at low energies, and describe an extension of this approximation which can help one to understand the resiliency of the valence quark model to meson loop corrections. He closes with a survey of issues that he hopes to see resolved before Baryon 2001.

Phase of the Wilson line at high temperature in the standard model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Korthals Altes, C.P.; Lee, K.; Pisarski, R.D.

1994-09-26

We compute the effective potential for the phase of the Wilson line at high temperature in the standard model to one-loop order. Besides the trivial vacua, there are metastable states in the direction of U(1) hypercharge. Assuming that the Universe starts out in such a metastable state at the Planck scale, it easily persists to the time of the electroweak phase transition, which then proceeds by an unusual mechanism. All remnants of the metastable state evaporate about the time of the QCD phase transition.

Baryon chiral perturbation theory combined with the 1 /Nc expansion in SU(3): Framework

NASA Astrophysics Data System (ADS)

Fernando, I. P.; Goity, J. L.

2018-03-01

Baryon chiral perturbation theory combined with the 1 /Nc expansion is implemented for three flavors. Baryon masses, vector charges and axial vector couplings are studied to one-loop and organized according to the ξ -expansion, in which the 1 /Nc and the low-energy power countings are linked according to 1 /Nc=O (ξ )=O (p ). The renormalization to O (ξ3) necessary for the mentioned observables is provided, along with applications to the baryon masses and axial couplings as obtained in lattice QCD calculations.

Biosynthesis and NMR-studies of a double transmembrane domain from the Y4 receptor, a human GPCR.

PubMed

Zou, Chao; Naider, Fred; Zerbe, Oliver

2008-12-01

The human Y4 receptor, a class A G-protein coupled receptor (GPCR) primarily targeted by the pancreatic polypeptide (PP), is involved in a large number of physiologically important functions. This paper investigates a Y4 receptor fragment (N-TM1-TM2) comprising the N-terminal domain, the first two transmembrane (TM) helices and the first extracellular loop followed by a (His)(6) tag, and addresses synthetic problems encountered when recombinantly producing such fragments from GPCRs in Escherichia coli. Rigorous purification and usage of the optimized detergent mixture 28 mM dodecylphosphocholine (DPC)/118 mM% 1-palmitoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)] (LPPG) resulted in high quality TROSY spectra indicating protein conformational homogeneity. Almost complete assignment of the backbone, including all TM residue resonances was obtained. Data on internal backbone dynamics revealed a high secondary structure content for N-TM1-TM2. Secondary chemical shifts and sequential amide proton nuclear Overhauser effects defined the TM helices. Interestingly, the properties of the N-terminal domain of this large fragment are highly similar to those determined on the isolated N-terminal domain in the presence of DPC micelles.

Posttranscriptional modifications in the A-loop of 23S rRNAs from selected archaea and eubacteria.

PubMed

Hansen, M A; Kirpekar, F; Ritterbusch, W; Vester, B

2002-02-01

Posttranscriptional modifications were mapped in helices 90-92 of 23S rRNA from the following phylogenetically diverse organisms: Haloarcula marismortui, Sulfolobus acidocaldarius, Bacillus subtilis, and Bacillus stearothermophilus. Helix 92 is a component of the ribosomal A-site, which contacts the aminoacyl-tRNA during protein synthesis, implying that posttranscriptional modifications in helices 90-92 may be important for ribosome function. RNA fragments were isolated from 23S rRNA by site-directed RNase H digestion. A novel method of mapping modifications by analysis of short, nucleotide-specific, RNase digestion fragments with Matrix Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS) was utilized. The MALDI-MS data were complemented by two primer extension techniques using reverse transcriptase. One technique utilizes decreasing concentrations of deoxynucleotide triphosphates to map 2'-O-ribose methylations. In the other, the rRNA is chemically modified, followed by mild alkaline hydrolysis to map pseudouridines (psis). A total of 10 posttranscriptionally methylated nucleotides and 6 psis were detected in the five organisms. Eight of the methylated nucleotides and one psi have not been reported previously. The distribution of modified nucleotides and their locations on the surface of the ribosomal peptidyl transferase cleft suggests functional importance.

A kMC-MD method with generalized move-sets for the simulation of folding of α-helical and β-stranded peptides.

PubMed

Peter, Emanuel K; Pivkin, Igor V; Shea, Joan-Emma

2015-04-14

In Monte-Carlo simulations of protein folding, pathways and folding times depend on the appropriate choice of the Monte-Carlo move or process path. We developed a generalized set of process paths for a hybrid kinetic Monte Carlo-Molecular dynamics algorithm, which makes use of a novel constant time-update and allows formation of α-helical and β-stranded secondary structures. We apply our new algorithm to the folding of 3 different proteins: TrpCage, GB1, and TrpZip4. All three systems are seen to fold within the range of the experimental folding times. For the β-hairpins, we observe that loop formation is the rate-determining process followed by collapse and formation of the native core. Cluster analysis of both peptides reveals that GB1 folds with equal likelihood along a zipper or a hydrophobic collapse mechanism, while TrpZip4 follows primarily a zipper pathway. The difference observed in the folding behavior of the two proteins can be attributed to the different arrangements of their hydrophobic core, strongly packed, and dry in case of TrpZip4, and partially hydrated in the case of GB1.

Two-phase pressure drop in a helical coil flow boiling system

NASA Astrophysics Data System (ADS)

Hardik, B. K.; Prabhu, S. V.

2018-05-01

The objective of the present work is to study the two-phase pressure drop in helical coils. Literature on the two-phase pressure drop in a helical coil suggests the complexity in flow boiling inside a helical coil due to secondary flow. Most of correlations reported in the literature on the two-phase pressure drop in a helical coil are limited to a specific operating range. No general correlation is available for a helical coil which is applicable for all fluids. In the present study, an experimental databank collected containing a total of 832 data points includes the data from the present study and from the literature. The data includes diabatic pressure drop of two fluids namely water and R123. Data covers a range of parameters namely a mass flux of 120-2058 kg/m2 s, a heat flux of 18-2831 kW/m2, an exit quality of 0.03-1, a density ratio of 32-1404 and a coil to tube diameter ratio of 14-58. The databank is compared with eighteen empirical correlations which include well referred correlations of straight tubes and the available correlations of helical coils. The straight tube correlations are not working well for the present data set. The helical coil correlations work reasonably well for the present databank. A correlation is suggested to predict the two-phase pressure drop in helical coils. The present study suggests that the influence of a helical coil is completely included in the single phase pressure drop correlation for helical coils.

Open and Lys–His Hexacoordinated Closed Structures of a Globin with Swapped Proximal and Distal Sites

PubMed Central

Teh, Aik-Hong; Saito, Jennifer A.; Najimudin, Nazalan; Alam, Maqsudul

2015-01-01

Globins are haem-binding proteins with a conserved fold made up of α-helices and can possess diverse properties. A putative globin-coupled sensor from Methylacidiphilum infernorum, HGbRL, contains an N-terminal globin domain whose open and closed structures reveal an untypical dimeric architecture. Helices E and F fuse into an elongated helix, resulting in a novel site-swapped globin fold made up of helices A–E, hence the distal site, from one subunit and helices F–H, the proximal site, from another. The open structure possesses a large cavity binding an imidazole molecule, while the closed structure forms a unique Lys–His hexacoordinated species, with the first turn of helix E unravelling to allow Lys52(E10) to bind to the haem. Ligand binding induces reorganization of loop CE, which is stabilized in the closed form, and helix E, triggering a large conformational movement in the open form. These provide a mechanical insight into how a signal may be relayed between the globin domain and the C-terminal domain of HGbRL, a Roadblock/LC7 domain. Comparison with HGbI, a closely related globin, further underlines the high degree of structural versatility that the globin fold is capable of, enabling it to perform a diversity of functions. PMID:26094577

Role of helicity in triad interactions in three-dimensional turbulence investigated by a new shell model

NASA Astrophysics Data System (ADS)

Rathmann, Nicholas M.; Ditlevsen, Peter D.

2016-09-01

Fully developed homogeneous isotropic turbulence in two dimensions is fundamentally different from that in three dimensions. In two dimensions, the simultaneous inviscid conservation of both kinetic energy and enstrophy within the inertial range of scales leads to a forward cascade of enstrophy and a reverse cascade of energy. In three dimensions, helicity, the integral of the scalar product of velocity and vorticity, is also an inviscid flow invariant along with the energy. Unlike the enstrophy, however, the helicity does not block the forward cascade of energy to small scales. Energy and helicity are conserved not only globally but also within each nonlinear triadic interaction between three plane waves in the spectral form of the Navier-Stokes equation (NSE). By decomposing each plane wave into two helical modes of opposite helicities, each triadic interaction is split into a set of eight helical triadic interactions between helical modes [F. Waleffe, Phys. Fluids A 4, 350 (1992), 10.1063/1.858309]. Recently it was found that a subset of these helical interactions, which render both signs of helicity separately conserved (enstrophy-like), leads to an inverse cascade of (part of) the energy [L. Biferale et al., Phys. Rev. Lett. 108, 164501 (2012), 10.1103/PhysRevLett.108.164501]. Motivated by this finding we introduce a new shell model, obtained from the NSE expressed in the helical basis, allowing the eight helical interactions to be coupled as in the NSE and their relative contributions evaluated as a function of both the net helicity input and triad geometry. By numerically integrating the new model, we find that the intermittency of the energy cascade decreases with the net helicity input. Studying the partitioning of the energy cascade between the eight helical interactions, we find that the decrease in intermittency is related to a shift in the dominating helical interactions when helically forced, two of which exhibit a larger cascade intermittency than the other six interactions. Among the relatively local triad geometries considered here, the partitioning of the energy and helicity cascades between the eight helical interactions shows no sign of change with triad geometry.

3′ Cap-Independent Translation Enhancers of Plant Viruses

PubMed Central

Simon, Anne E.; Miller, W. Allen

2014-01-01

In the absence of a 5′ cap, plant positive-strand RNA viruses have evolved a number of different elements in their 3′ untranslated region (UTR) to attract initiation factors and/or ribosomes to their templates. These 3′ cap-independent translational enhancers (3′ CITEs) take different forms, such as I-shaped, Y-shaped, T-shaped, or pseudoknotted structures, or radiate multiple helices from a central hub. Common features of most 3′ CITEs include the ability to bind a component of the translation initiation factor eIF4F complex and to engage in an RNA-RNA kissing-loop interaction with a hairpin loop located at the 5′ end of the RNA. The two T-shaped structures can bind to ribosomes and ribosomal subunits, with one structure also able to engage in a simultaneous long-distance RNA-RNA interaction. Several of these 3′ CITEs are interchangeable and there is evidence that natural recombination allows exchange of modular CITE units, which may overcome genetic resistance or extend the virus’s host range. PMID:23682606

The basic helix-loop-helix region of the transcriptional repressor hairy and enhancer of split 1 is preorganized to bind DNA.

PubMed

Popovic, Matija; Wienk, Hans; Coglievina, Maristella; Boelens, Rolf; Pongor, Sándor; Pintar, Alessandro

2014-04-01

Hairy and enhancer of split 1, one of the main downstream effectors in Notch signaling, is a transcriptional repressor of the basic helix-loop-helix (bHLH) family. Using nuclear magnetic resonance methods, we have determined the structure and dynamics of a recombinant protein, H1H, which includes an N-terminal segment, b1, containing functionally important phosphorylation sites, the basic region b2, required for binding to DNA, and the HLH domain. We show that a proline residue in the sequence divides the protein in two parts, a flexible and disordered N-terminal region including b1 and a structured, mainly helical region comprising b2 and the HLH domain. Binding of H1H to a double strand DNA oligonucleotide was monitored through the chemical shift perturbation of backbone amide resonances, and showed that the interaction surface involves not only the b2 segment but also several residues in the b1 and HLH regions. Copyright © 2014 Wiley Periodicals, Inc.

Hard Break-Up of Two-Nucleons and QCD Dynamics of NN Interaction

NASA Astrophysics Data System (ADS)

Sargsian, Misak; Granados, Carlos

2009-05-01

We investigate hard photodisintegration of two nucleons from ^3He nucleus within the framework of hard rescattering model (HRM). In HRM a quark of one nucleon knocked-out by incoming photon rescatters with a quark of the other nucleon leading to the production of two nucleons with high relative momentum. HRM allows to express the amplitude of two-nucleon break-up reaction through the convolution of photon-quark scattering, NN hard scattering amplitude and nuclear spectral function which can be calculated using nonrelativistic ^3He wave function. HRM predicts several specific features for hard break-up reaction. First, the cross section will approximately scale as s-11. Also one predicts comparable or larger cross section for pp break up as compared to that of pn break-up, which is opposite to what is observed in low energy kinematics. Another result is the prediction of different spectator momentum dependencies of pp and pn break-up cross sections. This is due to the fact that same-helicity pp-component is strongly suppressed in the ground state wave function of ^3He. Due to this suppression HRM predicts significantly different asymmetries for the cross section of polarization transfer NN break-up reactions for circularly polarized photons. For the pp break-up this asymmetry is predicted to be zero while for the pn it is close to 23.

New advances in the statistical parton distributions approach

NASA Astrophysics Data System (ADS)

Soffer, Jacques; Bourrely, Claude

2016-03-01

The quantum statistical parton distributions approach proposed more than one decade ago is revisited by considering a larger set of recent and accurate Deep Inelastic Scattering experimental results. It enables us to improve the description of the data by means of a new determination of the parton distributions. This global next-to-leading order QCD analysis leads to a good description of several structure functions, involving unpolarized parton distributions and helicity distributions, in terms of a rather small number of free parameters. There are many serious challenging issues. The predictions of this theoretical approach will be tested for single-jet production and charge asymmetry in W± production in p¯p and pp collisions up to LHC energies, using recent data and also for forthcoming experimental results. Presented by J. So.er at POETIC 2015

Two-fluid and finite Larmor radius effects on helicity evolution in a plasma pinch

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sauppe, J. P., E-mail: jpsauppe@gmail.com; Department of Physics, University of Wisconsin-Madison, 1150 University Avenue, Madison, Wisconsin 53706; Sovinec, C. R., E-mail: csovinec@wisc.edu

2016-03-15

The evolution of magnetic energy, helicity, and hybrid helicity during nonlinear relaxation of a driven-damped plasma pinch is compared in visco-resistive magnetohydrodynamics and two-fluid models with and without the ion gyroviscous stress tensor. Magnetic energy and helicity are supplied via a boundary electric field which initially balances the resistive dissipation, and the plasma undergoes multiple relaxation events during the nonlinear evolution. The magnetic helicity is well conserved relative to the magnetic energy over each event, which is short compared with the global resistive diffusion time. The magnetic energy decreases by roughly 1.5% of its initial value over a relaxation event,more » while the magnetic helicity changes by at most 0.2% of the initial value. The hybrid helicity is dominated by magnetic helicity in low-β pinch conditions and is also well conserved. Differences of less than 1% between magnetic helicity and hybrid helicity are observed with two-fluid modeling and result from cross helicity evolution. The cross helicity is found to change appreciably due to the first-order finite Larmor radius effects which have not been included in contemporary relaxation theories. The plasma current evolves towards the flat parallel current state predicted by Taylor relaxation theory but does not achieve it. Plasma flow develops significant structure for two-fluid models, and the flow perpendicular to the magnetic field is much more substantial than the flow along it.« less

SANC: the process γγ → ΖΖ

NASA Astrophysics Data System (ADS)

Bardin, D.; Bondarenko, S.; Christova, P.; Kalinovskaya, L.; von Schlippe, W.; Uglov, E.

2017-11-01

The implementation of the process γγ → ΖΖ at the one-loop level within SANC system multichannel approach is considered. The derived one-loop scalar form factors can be used for any cross channel after an appropriate permutation of their arguments-Mandelstam variables s, t, u. To check of the correctness of the results we observe the independence of the scalar form factors on the gauge parameters and the validity of Ward identity (external photon transversality). We present the complete analytical results for the covariant and tensor structures and helicity amplitudes for this process. We make an extensive comparison of our analytical and numerical results with those existing in the literature.

Identification of cisplatin-binding sites on the large cytoplasmic loop of the Na+/K+-ATPase.

PubMed

Šeflová, Jaroslava; Čechová, Petra; Štenclová, Tereza; Šebela, Marek; Kubala, Martin

2018-12-01

Cisplatin is the most widely used chemotherapeutic drug for the treatment of various types of cancer; however, its administration brings also numerous side effects. It was demonstrated that cisplatin can inhibit the Na + /K + -ATPase (NKA), which can explain a large part of the adverse effects. In this study, we have identified five cysteinyl residues (C452, C456, C457, C577, and C656) as the cisplatin binding sites on the cytoplasmic loop connecting transmembrane helices 4 and 5 (C45), using site-directed mutagenesis and mass spectrometry experiments. The identified residues are known to be susceptible to glutathionylation indicating their involvement in a common regulatory mechanism.

Extended investigation of the twelve-flavor β-function

NASA Astrophysics Data System (ADS)

Fodor, Zoltán; Holland, Kieran; Kuti, Julius; Nógrádi, Dániel; Wong, Chik Him

2018-04-01

We report new results from high precision analysis of an important BSM gauge theory with twelve massless fermion flavors in the fundamental representation of the SU(3) color gauge group. The range of the renormalized gauge coupling is extended from our earlier work [1] to probe the existence of an infrared fixed point (IRFP) in the β-function reported at two different locations, originally in [2] and at a new location in [3]. We find no evidence for the IRFP of the β-function in the extended range of the renormalized gauge coupling, in disagreement with [2,3]. New arguments to guard the existence of the IRFP remain unconvincing [4], including recent claims of an IRFP with ten massless fermion flavors [5,6] which we also rule out. Predictions of the recently completed 5-loop QCD β-function for general flavor number are discussed in this context.

Precision physics with QCD

NASA Astrophysics Data System (ADS)

Pich, Antonio

2017-03-01

The four-loop determination of the strong coupling from fully inclusive observables is reviewed. Special attention is given to the low-energy measurement extracted from the hadronic τ decay width. A recent exhaustive analysis of the ALEPH data, exploring several complementary methodologies with very different sensitivities to inverse power corrections and duality violations, confirms the strong suppression of non-perturbative contributions to Rτ. It gives the value αs(mτ2) = 0.328, which implies αs(MZ2) = 0.1197 ± 0.0015. The excellent agreement with the direct measurement at the Z peak, αs(MZ2) = 0.1196 ± 0.0030, provides a beautiful test of asymptotic freedom. Together with the most recent lattice average from FLAG and the NNLO determinations from e+e-, PDFs and collider data quoted by the PDG, these two inclusive determinations imply a world average value αs(MZ2) = 0.1180 ± 0.0010.

The structure of the ends of α-helices in globular proteins: effect of additional hydrogen bonds and implications for helix formation.

PubMed

Leader, David P; Milner-White, E James

2011-03-01

We prepared a set of about 2000 α-helices from a relational database of high-resolution three-dimensional structures of globular proteins, and identified additional main chain i ← i+3 hydrogen bonds at the ends of the helices (i.e., where the hydrogen bonding potential is not fulfilled by canonical i ← i+4 hydrogen bonds). About one-third of α-helices have such additional hydrogen bonds at the N-terminus, and more than half do so at the C-terminus. Although many of these additional hydrogen bonds at the C-terminus are associated with Schellman loops, the majority are not. We compared the dihedral angles at the termini of α-helices having or lacking the additional hydrogen bonds. Significant differences were found, especially at the C-terminus, where the dihedral angles at positions C2 and C1 in the absence of additional hydrogen bonds deviate substantially from those occurring within the α-helix. Using a novel approach we show how the structure of the C-terminus of the α-helix can emerge from that of constituent overlapping α-turns and β-turns, which individually show a variation in dihedral angles at different positions. We have also considered the direction of propagation of the α-helix using this approach. If one assumes that helices start as a single α-turn and grow by successive addition of further α-turns, the paths for growth in the N → C and C → N directions differ in a way that suggests that extension in the C → N direction is favored. Copyright © 2010 Wiley-Liss, Inc.

NMR studies of the dynamics of high-spin nitrophorins: comparative studies of NP4 and NP2 at close to physiological pH.

PubMed

Berry, Robert E; Muthu, Dhanasekaran; Yang, Fei; Walker, F Ann

2015-01-20

The β-barrel nitrophorin (NP) heme proteins are found in the saliva of the blood-sucking insect Rhodnius prolixus, which synthesizes and stores nitric oxide (NO) in the salivary glands. NO is bound to iron of the NPs and is released by dilution and an increase in pH when the insect spits its saliva into the tissues of a victim, to aid in obtaining a blood meal. In the adult insect, there are four nitrophorins, NP1-NP4, which have sequence similarities in two pairs, NP1 and NP4 (90% identical) and NP2 and NP3 (80% identical). The available crystal structures of NP4 have been used to propose that pH-dependent changes in the conformation of two loops between adjacent β-strands at the front opening of the protein, the A-B and G-H loops, determine the rate of NO release. At pH 7.3, NP4 releases NO 17 times faster than NP2 does. In this work, the aqua complexes of NP4 and NP2 have been investigated by nuclear magnetic resonance (NMR) relaxation measurements to probe the pico- to nanosecond and micro- to millisecond time scale motions at two pH values, 6.5 and 7.3. It is found that NP4-OH2 is fairly rigid and only residues in the loop regions show dynamics at pH 6.5; at pH 7.3, much more dynamics of the loops and most of the β-strands are observed while the α-helices remain fairly rigid. In comparison, NP2-OH2 shows much less dynamics, albeit somewhat more than that of the previously reported NP2-NO complex [Muthu, D., Berry, R. E., Zhang, H., and Walker, F. A. (2013) Biochemistry 52, 7910-7925]. The reasons for this major difference between NP4 and NP2 are discussed.

NMR Studies of the Dynamics of High-Spin Nitrophorins: Comparative Studies of NP4 and NP2 at Close to Physiological pH

PubMed Central

2015-01-01

The β-barrel nitrophorin (NP) heme proteins are found in the saliva of the blood-sucking insect Rhodnius prolixus, which synthesizes and stores nitric oxide (NO) in the salivary glands. NO is bound to iron of the NPs and is released by dilution and an increase in pH when the insect spits its saliva into the tissues of a victim, to aid in obtaining a blood meal. In the adult insect, there are four nitrophorins, NP1–NP4, which have sequence similarities in two pairs, NP1 and NP4 (90% identical) and NP2 and NP3 (80% identical). The available crystal structures of NP4 have been used to propose that pH-dependent changes in the conformation of two loops between adjacent β-strands at the front opening of the protein, the A–B and G–H loops, determine the rate of NO release. At pH 7.3, NP4 releases NO 17 times faster than NP2 does. In this work, the aqua complexes of NP4 and NP2 have been investigated by nuclear magnetic resonance (NMR) relaxation measurements to probe the pico- to nanosecond and micro- to millisecond time scale motions at two pH values, 6.5 and 7.3. It is found that NP4-OH2 is fairly rigid and only residues in the loop regions show dynamics at pH 6.5; at pH 7.3, much more dynamics of the loops and most of the β-strands are observed while the α-helices remain fairly rigid. In comparison, NP2-OH2 shows much less dynamics, albeit somewhat more than that of the previously reported NP2-NO complex [Muthu, D., Berry, R. E., Zhang, H., and Walker, F. A. (2013) Biochemistry 52, 7910–7925]. The reasons for this major difference between NP4 and NP2 are discussed. PMID:25486224

Lattice QCD static potentials of the meson-meson and tetraquark systems computed with both quenched and full QCD

NASA Astrophysics Data System (ADS)

Bicudo, P.; Cardoso, M.; Oliveira, O.; Silva, P. J.

2017-10-01

We revisit the static potential for the Q Q Q ¯Q ¯ system using SU(3) lattice simulations, studying both the color singlets' ground state and first excited state. We consider geometries where the two static quarks and the two antiquarks are at the corners of rectangles of different sizes. We analyze the transition between a tetraquark system and a two-meson system with a two by two correlator matrix. We compare the potentials computed with quenched QCD and with dynamical quarks. We also compare our simulations with the results of previous studies and analyze quantitatively fits of our results with Ansätze inspired in the string flip-flop model and in its possible color excitations.

Generalized parton distributions and transversity from full lattice QCD

NASA Astrophysics Data System (ADS)

Göckeler, M.; Hägler, Ph.; Horsley, R.; Pleiter, D.; Rakow, P. E. L.; Schäfer, A.; Schierholz, G.; Zanotti, J. M.; Qcdsf Collaboration

2005-06-01

We present here the latest results from the QCDSF collaboration for moments of gener- alized parton distributions and transversity in two-flavour QCD, including a preliminary analysis of the pion mass dependence.

A unified convention for biological assemblies with helical symmetry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsai, Chung-Jung, E-mail: tsaic@mail.nih.gov; Nussinov, Ruth; Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978

A new representation of helical structure by four parameters, [n{sub 1}, n{sub 2}, twist, rise], is able to generate an entire helical construct from asymmetric units, including cases of helical assembly with a seam. Assemblies with helical symmetry can be conveniently formulated in many distinct ways. Here, a new convention is presented which unifies the two most commonly used helical systems for generating helical assemblies from asymmetric units determined by X-ray fibre diffraction and EM imaging. A helical assembly is viewed as being composed of identical repetitive units in a one- or two-dimensional lattice, named 1-D and 2-D helical systems,more » respectively. The unification suggests that a new helical description with only four parameters [n{sub 1}, n{sub 2}, twist, rise], which is called the augmented 1-D helical system, can generate the complete set of helical arrangements, including coverage of helical discontinuities (seams). A unified four-parameter characterization implies similar parameters for similar assemblies, can eliminate errors in reproducing structures of helical assemblies and facilitates the generation of polymorphic ensembles from helical atomic models or EM density maps. Further, guidelines are provided for such a unique description that reflects the structural signature of an assembly, as well as rules for manipulating the helical symmetry presentation.« less

Second-order QCD effects in Higgs boson production through vector boson fusion

NASA Astrophysics Data System (ADS)

Cruz-Martinez, J.; Gehrmann, T.; Glover, E. W. N.; Huss, A.

2018-06-01

We compute the factorising second-order QCD corrections to the electroweak production of a Higgs boson through vector boson fusion. Our calculation is fully differential in the kinematics of the Higgs boson and of the final state jets, and uses the antenna subtraction method to handle infrared singular configurations in the different parton-level contributions. Our results allow us to reassess the impact of the next-to-leading order (NLO) QCD corrections to electroweak Higgs-plus-three-jet production and of the next-to-next-to-leading order (NNLO) QCD corrections to electroweak Higgs-plus-two-jet production. The NNLO corrections are found to be limited in magnitude to around ± 5% and are uniform in several of the kinematical variables, displaying a kinematical dependence only in the transverse momenta and rapidity separation of the two tagging jets.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dudek, Jozef

Highlights of the research include: the determination of the form of the lowest energy gluonic excitation within QCD and the spectrum of hybrid hadrons which follows; the first calculation of the spectrum of hybrid baryons within a first-principles approach to QCD; a detailed mapping out of the phase-shift of elastic ππ scattering featuring the ρ resonance at two values of the light quark mass within lattice QCD; the first (and to date, only) determinations of coupled-channel meson-meson scattering within first-principles QCD; the first (and to date, only) determinations of the radiative coupling of a resonant state, the ρ appearing inmore » πγ→ππ; the first (and to date, only) determination of the properties of the broad σ resonance in elastic ππ scattering within QCD without unjustified approximations.« less

Attenuation of Phosphorylation-dependent Activation of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) by Disease-causing Mutations at the Transmission Interface*

PubMed Central

Chin, Stephanie; Yang, Donghe; Miles, Andrew J.; Eckford, Paul D. W.; Molinski, Steven; Wallace, B. A.; Bear, Christine E.

2017-01-01

Cystic fibrosis transmembrane conductance regulator (CFTR) is a multidomain membrane protein that functions as a phosphorylation-regulated anion channel. The interface between its two cytosolic nucleotide binding domains and coupling helices conferred by intracellular loops extending from the channel pore domains has been referred to as a transmission interface and is thought to be critical for the regulated channel activity of CFTR. Phosphorylation of the regulatory domain of CFTR by protein kinase A (PKA) is required for its channel activity. However, it was unclear if phosphorylation modifies the transmission interface. Here, we studied purified full-length CFTR protein using spectroscopic techniques to determine the consequences of PKA-mediated phosphorylation. Synchrotron radiation circular dichroism spectroscopy confirmed that purified full-length wild-type CFTR is folded and structurally responsive to phosphorylation. Intrinsic tryptophan fluorescence studies of CFTR showed that phosphorylation reduced iodide-mediated quenching, consistent with an effect of phosphorylation in burying tryptophans at the transmission interface. Importantly, the rate of phosphorylation-dependent channel activation was compromised by the introduction of disease-causing mutations in either of the two coupling helices predicted to interact with nucleotide binding domain 1 at the interface. Together, these results suggest that phosphorylation modifies the interface between the catalytic and pore domains of CFTR and that this modification facilitates CFTR channel activation. PMID:28003367

Topology mapping to characterize cyanobacterial bicarbonate transporters: BicA (SulP/SLC26 family) and SbtA.

PubMed

Price, G Dean; Howitt, Susan M

2014-09-01

This mini-review addresses advances in understanding the transmembrane topologies of two unrelated, single-subunit bicarbonate transporters from cyanobacteria, namely BicA and SbtA. BicA is a Na(+)-dependent bicarbonate transporter that belongs to the SulP/SLC26 family that is widespread in both eukaryotes and prokaryotes. Topology mapping of BicA via the phoA/lacZ fusion reporter method identified 12 transmembrane helices with an unresolved hydrophobic region just beyond helix 8. Re-interpreting this data in the light of a recent topology study on rat prestin leads to a consensus topology of 14 transmembrane domains with a 7+7 inverted repeat structure. SbtA is also a Na(+)-dependent bicarbonate transporter, but of considerably higher affinity (Km 2-5 μM versus >100 μM for BicA). Whilst SbtA is widespread in cyanobacteria and a few bacteria, it appears to be absent from eukaryotes. Topology mapping of SbtA via the phoA/lacZ fusion reporter method identified 10 transmembrane helices. The topology consists of a 5+5 inverted repeat, with the two repeats separated by a large intracellular loop. The unusual location of the N and C-termini outside the cell raises the possibility that SbtA forms a novel fold, not so far identified by structural and topological studies on transport proteins.

Experimental demonstration of plasma startup by coaxial helicity injection

NASA Astrophysics Data System (ADS)

Raman, R.; Jarboe, T. R.; Nelson, B. A.; Hamp, W. T.; Izzo, V. A.; O'Neill, R. G.; Redd, A. J.; Sieck, P. E.; Smith, R. J.

2004-05-01

Experimental results on the transfer of a coaxial-helicity-injection (CHI) produced discharge to inductive operation are reported. CHI assisted plasma startup is more robust than inductive only operation and reduces volt-seconds consumption. After handoff to inductive operation, the initial 100 kA of CHI produced current drops to 50 kA, then ramps up to 180 kA, using only 30 mVs, about 40% higher than that produced by induction alone. Results show that initiation of CHI discharges at lower densities produce higher levels of coupling current. Coupling a CHI produced discharge to induction from a precharged central solenoid has produced record currents of 290 kA using only 52 mWb of central solenoid flux. CHI discharges can also be generated while the central transformer is in the process of being precharged, during which period it induces a negative loop voltage on the CHI discharge. These significant results were obtained on the Helicity Injected Torus-II (HIT-II) [T.R. Jarboe, Fusion Technol. 15, 7 (1989)] spherical torus experiment (major/minor radius of 0.3/0.2 m and elongation of 1.5).

Local conformational dynamics in alpha-helices measured by fast triplet transfer.

PubMed

Fierz, Beat; Reiner, Andreas; Kiefhaber, Thomas

2009-01-27

Coupling fast triplet-triplet energy transfer (TTET) between xanthone and naphthylalanine to the helix-coil equilibrium in alanine-based peptides allowed the observation of local equilibrium fluctuations in alpha-helices on the nanoseconds to microseconds time scale. The experiments revealed faster helix unfolding in the terminal regions compared with the central parts of the helix with time constants varying from 250 ns to 1.4 micros at 5 degrees C. Local helix formation occurs with a time constant of approximately 400 ns, independent of the position in the helix. Comparing the experimental data with simulations using a kinetic Ising model showed that the experimentally observed dynamics can be explained by a 1-dimensional boundary diffusion with position-independent elementary time constants of approximately 50 ns for the addition and of approximately 65 ns for the removal of an alpha-helical segment. The elementary time constant for helix growth agrees well with previously measured time constants for formation of short loops in unfolded polypeptide chains, suggesting that helix elongation is mainly limited by a conformational search.

Bak Conformational Changes Induced by Ligand Binding: Insight into BH3 Domain Binding and Bak Homo-Oligomerization

PubMed Central

Pang, Yuan-Ping; Dai, Haiming; Smith, Alyson; Meng, X. Wei; Schneider, Paula A.; Kaufmann, Scott H.

2012-01-01

Recently we reported that the BH3-only proteins Bim and Noxa bind tightly but transiently to the BH3-binding groove of Bak to initiate Bak homo-oligomerization. However, it is unclear how such tight binding can induce Bak homo-oligomerization. Here we report the ligand-induced Bak conformational changes observed in 3D models of Noxa·Bak and Bim·Bak refined by molecular dynamics simulations. In particular, upon binding to the BH3-binding groove, Bim and Noxa induce a large conformational change of the loop between helices 1 and 2 and in turn partially expose a remote groove between helices 1 and 6 in Bak. These observations, coupled with the reported experimental data, suggest formation of a pore-forming Bak octamer, in which the BH3-binding groove is at the interface on one side of each monomer and the groove between helices 1 and 6 is at the interface on the opposite side, initiated by ligand binding to the BH3-binding groove. PMID:22355769

QCD Condensates and Holographic Wilson Loops for Asymptotically AdS Spaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Quevedo, R. Carcasses; Goity, Jose L.; Trinchero, Roberto C.

2014-02-01

The minimization of the Nambu-Goto (NG) action for a surface whose contour defines a circular Wilson loop of radius a placed at a finite value of the coordinate orthogonal to the border is considered. This is done for asymptotically AdS spaces. The condensates of dimension n = 2, 4, 6, 8, and 10 are calculated in terms of the coefficients in the expansion in powers of the radius a of the on-shell subtracted NG action for small a->0. The subtraction employed is such that it presents no conflict with conformal invariance in the AdS case and need not introduce anmore » additional infrared scale for the case of confining geometries. It is shown that the UV value of the gluon condensates is universal in the sense that it only depends on the first coefficients of the difference with the AdS case.« less

Conjecture about the 2-Flavour QCD Phase Diagram

NASA Astrophysics Data System (ADS)

Nava Blanco, M. A.; Bietenholz, W.; Fernández Téllez, A.

2017-10-01

The QCD phase diagram, in particular its sector of high baryon density, is one of the most prominent outstanding mysteries within the Standard Model of particle physics. We sketch a project how to arrive at a conjecture for the case of two massless quark flavours. The pattern of spontaneous chiral symmetry breaking is isomorphic to the spontaneous magnetisation in an O(4) non-linear σ-model, which can be employed as a low-energy effective theory to study the critical behaviour. We focus on the 3d O(4) model, where the configurations are divided into topological sectors, as in QCD. A topological winding with minimal Euclidean action is denoted as a skyrmion, and the topological charge corresponds to the QCD baryon number. This effective model can be simulated on a lattice with a powerful cluster algorithm, which should allow us to identify the features of the critical temperature, as we proceed from low to high baryon density. In this sense, this projected numerical study has the potential to provide us with a conjecture about the phase diagram of QCD with two massless quark flavours.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lello, Louis; Boyanovsky, Daniel; Pisarski, Robert D.

Here, in the standard model extended with a seesaw mass matrix, we study the production of sterile neutrinos from the decay of vector bosons at temperatures near the masses of the electroweak bosons. We derive a general quantum kinetic equation for the production of sterile neutrinos and their effective mixing angles, which is applicable over a wide range of temperature, to all orders in interactions of the standard model and to leading order in a small mixing angle for the neutrinos. We emphasize the relation between the production rate and Landau damping at one-loop order and show that production rates and effective mixing angles depend sensitively upon the neutrino’s helicity. Sterile neutrinos with positive helicity interact more weakly with the medium than those with negative helicity, and their effective mixing angle is not modified significantly. Negative helicity states couple more strongly to the vector bosons, but their mixing angle is strongly suppressed by the medium. Consequently, if the mass of the sterile neutrino is ≲ 8.35 MeV , there are fewer states with negative helicity produced than those with positive helicity. There is an Mikheyev-Smirnov-Wolfenstein-type resonance in the absence of lepton asymmetry, but due to screening by the damping rate, the production rate is not enhanced. Sterile neutrinos with negative helicity freeze out at Tmore » $$-\\atop{f}$$ ≃ 5 GeV , whereas positive helicity neutrinos freeze out at T$$+\\atop{f}$$≃ 8 GeV , with both distributions far from thermal. As the temperature decreases, due to competition between a decreasing production rate and an increasing mixing angle, the distribution function for states with negative helicity is broader in momentum and hotter than that for those with positive helicity. Sterile neutrinos produced via vector boson decay do not satisfy the abundance, lifetime, and cosmological constraints to be the sole dark matter component in the Universe. Massive sterile neutrinos produced via vector boson decay might solve the 7Li problem, albeit at the very edge of the possible parameter space. A heavy sterile neutrino with a mass of a few MeV could decay into light sterile neutrinos, of a few keV in mass, that contribute to warm dark matter. In conclusion, we argue that heavy sterile neutrinos with lifetime ≤1/H 0 reach local thermodynamic equilibrium.« less

Production of heavy sterile neutrinos from vector boson decay at electroweak temperatures

NASA Astrophysics Data System (ADS)

Lello, Louis; Boyanovsky, Daniel; Pisarski, Robert D.

2017-02-01

In the standard model extended with a seesaw mass matrix, we study the production of sterile neutrinos from the decay of vector bosons at temperatures near the masses of the electroweak bosons. We derive a general quantum kinetic equation for the production of sterile neutrinos and their effective mixing angles, which is applicable over a wide range of temperature, to all orders in interactions of the standard model and to leading order in a small mixing angle for the neutrinos. We emphasize the relation between the production rate and Landau damping at one-loop order and show that production rates and effective mixing angles depend sensitively upon the neutrino's helicity. Sterile neutrinos with positive helicity interact more weakly with the medium than those with negative helicity, and their effective mixing angle is not modified significantly. Negative helicity states couple more strongly to the vector bosons, but their mixing angle is strongly suppressed by the medium. Consequently, if the mass of the sterile neutrino is ≲8.35 MeV , there are fewer states with negative helicity produced than those with positive helicity. There is an Mikheyev-Smirnov-Wolfenstein-type resonance in the absence of lepton asymmetry, but due to screening by the damping rate, the production rate is not enhanced. Sterile neutrinos with negative helicity freeze out at Tf-≃5 GeV , whereas positive helicity neutrinos freeze out at Tf+≃8 GeV , with both distributions far from thermal. As the temperature decreases, due to competition between a decreasing production rate and an increasing mixing angle, the distribution function for states with negative helicity is broader in momentum and hotter than that for those with positive helicity. Sterile neutrinos produced via vector boson decay do not satisfy the abundance, lifetime, and cosmological constraints to be the sole dark matter component in the Universe. Massive sterile neutrinos produced via vector boson decay might solve the 7Li problem, albeit at the very edge of the possible parameter space. A heavy sterile neutrino with a mass of a few MeV could decay into light sterile neutrinos, of a few keV in mass, that contribute to warm dark matter. We argue that heavy sterile neutrinos with lifetime ≤1 /H0 reach local thermodynamic equilibrium.

Production of heavy sterile neutrinos from vector boson decay at electroweak temperatures

DOE PAGES

Lello, Louis; Boyanovsky, Daniel; Pisarski, Robert D.

2017-02-22

Here, in the standard model extended with a seesaw mass matrix, we study the production of sterile neutrinos from the decay of vector bosons at temperatures near the masses of the electroweak bosons. We derive a general quantum kinetic equation for the production of sterile neutrinos and their effective mixing angles, which is applicable over a wide range of temperature, to all orders in interactions of the standard model and to leading order in a small mixing angle for the neutrinos. We emphasize the relation between the production rate and Landau damping at one-loop order and show that production rates and effective mixing angles depend sensitively upon the neutrino’s helicity. Sterile neutrinos with positive helicity interact more weakly with the medium than those with negative helicity, and their effective mixing angle is not modified significantly. Negative helicity states couple more strongly to the vector bosons, but their mixing angle is strongly suppressed by the medium. Consequently, if the mass of the sterile neutrino is ≲ 8.35 MeV , there are fewer states with negative helicity produced than those with positive helicity. There is an Mikheyev-Smirnov-Wolfenstein-type resonance in the absence of lepton asymmetry, but due to screening by the damping rate, the production rate is not enhanced. Sterile neutrinos with negative helicity freeze out at Tmore » $$-\\atop{f}$$ ≃ 5 GeV , whereas positive helicity neutrinos freeze out at T$$+\\atop{f}$$≃ 8 GeV , with both distributions far from thermal. As the temperature decreases, due to competition between a decreasing production rate and an increasing mixing angle, the distribution function for states with negative helicity is broader in momentum and hotter than that for those with positive helicity. Sterile neutrinos produced via vector boson decay do not satisfy the abundance, lifetime, and cosmological constraints to be the sole dark matter component in the Universe. Massive sterile neutrinos produced via vector boson decay might solve the 7Li problem, albeit at the very edge of the possible parameter space. A heavy sterile neutrino with a mass of a few MeV could decay into light sterile neutrinos, of a few keV in mass, that contribute to warm dark matter. In conclusion, we argue that heavy sterile neutrinos with lifetime ≤1/H 0 reach local thermodynamic equilibrium.« less

Modeling the small dark energy scale with a quintessential pseudoscalar boson

NASA Astrophysics Data System (ADS)

Kim, Jihn E.

2014-03-01

Democracy among the same type of particles is a useful paradigm in studying masses and interactions of particles with supersymmetry (SUSY) or without SUSY. This simple idea predicts the presence of massless particles. We attempt to use one of these massless pseudoscalar particles to generate the cosmological dark energy (DE) potential. To achieve the extremely shallow potential of DE, we require the pseudoscalar boson not couple to quantum chromodynamics (QCD) anomaly. Thus, we consider two pseudoscalars, one coupling to the QCD anomaly ( i.e., the QCD axion) and the other not coupling to the QCD anomaly. To obtain these two pseudoscalars, we introduce two approximate global U(1) symmetries to realize them as the pseudo-Goldstone bosons of the spontaneously broken U(1) symmetries. These global symmetries are dictated by a gravity-respecting discrete symmetry. Specifically, we consider an S 2( L) × S 2( R) × Z 10 R example and attempt to obtain the DE scale in terms of two observed fundamental mass scales, the grand unification scale M G and the electroweak scale υ ew.

How perfect can a gluon plasma be in perturbative QCD?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Jiunn-Wei; Deng Jian; Dong Hui

2011-02-01

The shear viscosity to entropy density ratio, {eta}/s, characterizes how perfect a fluid is. We calculate the leading order {eta}/s of a gluon plasma in perturbation using the kinetic theory. The leading order contribution only involves the elastic gg{r_reversible}gg (22) process and the inelastic gg{r_reversible}ggg (23) process. The hard-thermal-loop (HTL) treatment is used for the 22 matrix element, while the exact matrix element in vacuum is supplemented by the gluon Debye mass insertion for the 23 process. Also, the asymptotic mass is used for the external gluons in the kinetic theory. The errors from not implementing HTL and the Landau-Pomeranchuk-Migdalmore » effect in the 23 process, and from the uncalculated higher order corrections, are estimated. Our result smoothly connects the two different approximations used by Arnold, Moore, and Yaffe (AMY) and Xu and Greiner (XG). At small {alpha}{sub s} ({alpha}{sub s}<<1), our result is closer to AMY's collinear result while at larger {alpha}{sub s} the finite angle noncollinear configurations become more important and our result is closer to XG's soft bremsstrahlung result. In the region where perturbation is reliable ({alpha}{sub s} < or approx. 0.1), we find no indication that the proposed perfect fluid limit {eta}/s{approx_equal}1/(4{pi}) can be achieved by perturbative QCD alone. Whether this can be achieve for {alpha}{sub s} > or approx. 0.1 is still an open question.« less

Microstructure evolution of recrystallized Zircaloy-4 under charged particles irradiation

NASA Astrophysics Data System (ADS)

Gaumé, M.; Onimus, F.; Dupuy, L.; Tissot, O.; Bachelet, C.; Mompiou, F.

2017-11-01

Recrystallized zirconium alloys are used as nuclear fuel cladding tubes of Pressurized Water Reactors. During operation, these alloys are submitted to fast neutron irradiation which leads to their in-reactor deformation and to a change of their mechanical properties. These phenomena are directly related to the microstructure evolution under irradiation and especially to the formation of -type dislocation loops. In the present work, the radiation damage evolution in recrystallized Zircaloy-4 has been studied using charged particles irradiation. The loop nucleation and growth kinetics, and also the helical climb of linear dislocations, were observed in-situ using a High Voltage Electron Microscope (HVEM) under 1 MeV electron irradiation at 673 and 723 K. In addition, 600 keV Zr+ ion irradiations were conducted at the same temperature. Transmission Electron Microscopy (TEM) characterizations have been performed after both types of irradiations, and show dislocation loops with a Burgers vector belonging to planes close to { 10 1 bar 0 } first order prismatic planes. The nature of the loops has been characterized. Only interstitial dislocation loops have been observed after ion irradiation at 723 K. However, after electron irradiation conducted at 673 and 723 K, both interstitial and vacancy loops were observed, the proportion of interstitial loops increasing as the temperature is increased. The loop growth kinetics analysis shows that as the temperature increases, the loop number density decreases and the loop growth rate tends to increase. An increase of the flux leads to an increase of the loop number density and a decrease of the loop growth rate. The results are compared to previous works and discussed in the light of point defects diffusion.

TORNADO-LIKE EVOLUTION OF A KINK-UNSTABLE SOLAR PROMINENCE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Wensi; Liu, Rui; Wang, Yuming, E-mail: rliu@ustc.edu.cn

We report on the tornado-like evolution of a quiescent prominence on 2014 November 1. The eastern section of the prominence first rose slowly, transforming into an arch-shaped structure as high as ∼150 Mm above the limb; the arch then writhed moderately in a left-handed sense, while the original dark prominence material emitted in the Fe ix 171 Å passband, and a braided structure appeared at the eastern edge of the warped arch. The unraveling of the braided structure was associated with a transient brightening in the EUV and apparently contributed to the formation of a curtain-like structure (CLS). The CLSmore » consisted of myriad thread-like loops rotating counterclockwise about the vertical if viewed from above. Heated prominence material was observed to slide along these loops and land outside the filament channel. The tornado eventually disintegrated and the remaining material flew along a left-handed helical path constituting approximately a full turn, as corroborated through stereoscopic reconstruction, into the cavity of the stable, western section of the prominence. We suggest that the tornado-like evolution of the prominence was governed by the helical kink instability, and that the CLS formed through magnetic reconnections between the prominence field and the overlying coronal field.« less

A mock heart engineered with helical aramid fibers for in vitro cardiovascular device testing.

PubMed

Jansen-Park, So-Hyun; Hsu, Po-Lin; Müller, Indra; Steinseifer, Ulrich; Abel, Dirk; Autschbach, Rüdiger; Rossaint, Rolf; Schmitz-Rode, Thomas

2017-04-01

Mock heart circulation loops (MHCLs) serve as in-vitro platforms to investigate the physiological interaction between circulatory systems and cardiovascular devices. A mock heart (MH) engineered with silicone walls and helical aramid fibers, to mimic the complex contraction of a natural heart, has been developed to advance the MHCL previously developed in our group. A mock aorta with an anatomical shape enables the evaluation of a cannulation method for ventricular assist devices (VADs) and investigation of the usage of clinical measurement systems like pressure-volume catheters. Ventricle and aorta molds were produced based on MRI data and cast with silicone. Aramid fibers were layered in the silicone ventricle to reproduce ventricle torsion. A rotating hollow shaft was connected to the apex enabling the rotation of the MH and the connection of a VAD. Silicone wall thickness, aramid fiber angle and fiber pitch were varied to generate different MH models. All MH models were placed in a tank filled with variable amounts of water and air simulating the compliance. In this work, physiological ventricular torsion angles (15°-26°) and physiological pressure-volume loops were achieved. This MHCL can serve as a comprehensive testing platform for cardiovascular devices, such as artificial heart valves and cannulation of VADs.

Susceptibility of the QCD vacuum to CP-odd electromagnetic background fields.

PubMed

D'Elia, Massimo; Mariti, Marco; Negro, Francesco

2013-02-22

We investigate two flavor quantum chromodynamics (QCD) in the presence of CP-odd electromagnetic background fields and determine, by means of lattice QCD simulations, the induced effective θ term to first order in E[over →] · B[over →]. We employ a rooted staggered discretization and study lattice spacings down to 0.1 fm and Goldstone pion masses around 480 MeV. In order to deal with a positive measure, we consider purely imaginary electric fields and real magnetic fields, and then exploit the analytic continuation. Our results are relevant to a description of the effective pseudoscalar quantum electrodynamics-QCD interactions.

Renormalizable Quantum Field Theories in the Large -n Limit

NASA Astrophysics Data System (ADS)

Guruswamy, Sathya

1995-01-01

In this thesis, we study two examples of renormalizable quantum field theories in the large-N limit. Chapter one is a general introduction describing physical motivations for studying such theories. In chapter two, we describe the large-N method in field theory and discuss the pioneering work of 't Hooft in large-N two-dimensional Quantum Chromodynamics (QCD). In chapter three we study a spherically symmetric approximation to four-dimensional QCD ('spherical QCD'). We recast spherical QCD into a bilocal (constrained) theory of hadrons which in the large-N limit is equivalent to large-N spherical QCD for all energy scales. The linear approximation to this theory gives an eigenvalue equation which is the analogue of the well-known 't Hooft's integral equation in two dimensions. This eigenvalue equation is a scale invariant one and therefore leads to divergences in the theory. We give a non-perturbative renormalization prescription to cure this and obtain a beta function which shows that large-N spherical QCD is asymptotically free. In chapter four, we review the essentials of conformal field theories in two and higher dimensions, particularly in the context of critical phenomena. In chapter five, we study the O(N) non-linear sigma model on three-dimensional curved spaces in the large-N limit and show that there is a non-trivial ultraviolet stable critical point at which it becomes conformally invariant. We study this model at this critical point on examples of spaces of constant curvature and compute the mass gap in the theory, the free energy density (which turns out to be a universal function of the information contained in the geometry of the manifold) and the two-point correlation functions. The results we get give an indication that this model is an example of a three-dimensional analogue of a rational conformal field theory. A conclusion with a brief summary and remarks follows at the end.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rushton, Phillip S.; Olek, Anna T.; Makowski, Lee

The crystallographic structure of a rice (Oryza sativa) cellulose synthase, OsCesA8, plant-conserved region (P-CR), one of two unique domains in the catalytic domain of plant CesAs, was solved to 2.4 Å resolution. Two antiparallel α-helices form a coiled-coil domain linked by a large extended connector loop containing a conserved trio of aromatic residues. The P-CR structure was fit into a molecular envelope for the P-CR domain derived from small-angle X-ray scattering data. The P-CR structure and molecular envelope, combined with a homology-based chain trace of the CesA8 catalytic core, were modeled into a previously determined CesA8 small-angle X-ray scattering molecularmore » envelope to produce a detailed topological model of the CesA8 catalytic domain. The predicted position for the P-CR domain from the molecular docking models places the P-CR connector loop into a hydrophobic pocket of the catalytic core, with the coiled-coil aligned near the entrance of the substrate UDP-glucose into the active site. In this configuration, the P-CR coiled-coil alone is unlikely to regulate substrate access to the active site, but it could interact with other domains of CesA, accessory proteins, or other CesA catalytic domains to control substrate delivery.« less

Rescattering Effects in the Hadronic-Light-by-Light Contribution to the Anomalous Magnetic Moment of the Muon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Colangelo, Gilberto; Hoferichter, Martin; Procura, Massimiliano

We present a first model-independent calculation of ππ intermediate states in the hadronic-light-by-light (HLBL) contribution to the anomalous magnetic moment of the muon (g - 2) μ that goes beyond the scalar QED pion loop. To this end, we combine a recently developed dispersive description of the HLBL tensor with a partial-wave expansion and demonstrate that the known scalar-QED result is recovered after partial-wave resummation. Using dispersive fits to high-statistics data for the pion vector form factor, we provide an evaluation of the full pion box a π μ box = –15.9(2) x 10 -11. We then construct a suitablemore » input for the γ*γ* → ππ helicity partial waves, based on a pion-pole left-hand cut and show that for the dominant charged-pion contribution, this representation is consistent with the two-loop chiral prediction and the COMPASS measurement for the pion polarizability. This allows us to reliably estimate S-wave rescattering effects to the full pion box and leads to our final estimate for the sum of these two contributions a π μ box + a ππ,π-pole μ,J=0 LHC = –24(1) x 10 -11.« less

Rescattering Effects in the Hadronic-Light-by-Light Contribution to the Anomalous Magnetic Moment of the Muon

DOE PAGES

Colangelo, Gilberto; Hoferichter, Martin; Procura, Massimiliano; ...

2017-06-09

We present a first model-independent calculation of ππ intermediate states in the hadronic-light-by-light (HLBL) contribution to the anomalous magnetic moment of the muon (g - 2) μ that goes beyond the scalar QED pion loop. To this end, we combine a recently developed dispersive description of the HLBL tensor with a partial-wave expansion and demonstrate that the known scalar-QED result is recovered after partial-wave resummation. Using dispersive fits to high-statistics data for the pion vector form factor, we provide an evaluation of the full pion box a π μ box = –15.9(2) x 10 -11. We then construct a suitablemore » input for the γ*γ* → ππ helicity partial waves, based on a pion-pole left-hand cut and show that for the dominant charged-pion contribution, this representation is consistent with the two-loop chiral prediction and the COMPASS measurement for the pion polarizability. This allows us to reliably estimate S-wave rescattering effects to the full pion box and leads to our final estimate for the sum of these two contributions a π μ box + a ππ,π-pole μ,J=0 LHC = –24(1) x 10 -11.« less

Current matrix element in HAL QCD's wavefunction-equivalent potential method

NASA Astrophysics Data System (ADS)

Watanabe, Kai; Ishii, Noriyoshi

2018-04-01

We give a formula to calculate a matrix element of a conserved current in the effective quantum mechanics defined by the wavefunction-equivalent potentials proposed by the HAL QCD collaboration. As a first step, a non-relativistic field theory with two-channel coupling is considered as the original theory, with which a wavefunction-equivalent HAL QCD potential is obtained in a closed analytic form. The external field method is used to derive the formula by demanding that the result should agree with the original theory. With this formula, the matrix element is obtained by sandwiching the effective current operator between the left and right eigenfunctions of the effective Hamiltonian associated with the HAL QCD potential. In addition to the naive one-body current, the effective current operator contains an additional two-body term emerging from the degrees of freedom which has been integrated out.

Site-directed mutagenesis of the hinge peptide from the hemagglutinin protein: enhancement of the pH-responsive conformational change.

PubMed

Casali, Monica; Banta, Scott; Zambonelli, Carlo; Megeed, Zaki; Yarmush, Martin L

2008-06-01

Environmentally responsive proteins and peptides are increasingly finding utility in various engineered systems due to their ability to respond to the presentation of external stimuli. A classic example of this behavior is the influenza hemagglutinin (HA) fusion protein. At neutral pH, HA exists in a non-fusogenic state, but upon exposure to low pH, the conformation of the structure changes to expose a fusogenic peptide. During this structural change, massive rearrangements occur in a subunit of HA (HA2). Crystallography data has shown that a loop of 28 amino acids (residues 54-81) undergoes a dramatic transition from a random coil to an alpha-helix. This segment connects to two flanking helical regions (short and long) to form a long, continuous helix. Here, we report the results of site-directed mutagenesis study on LOOP-36 to further understand the mechanism of this important stimulus-responsive peptide. The conformational transition of a bacterially expressed LOOP-36 was found to be less dramatic than has been previously reported. The systematic mutation of glutamate and histidine residues in the peptide to glutamines (glutamine scanning) did not impact the conformational behavior of the peptide, but the substitution of the glycine residue at position 22 with alanine resulted in significant pH-responsive behavior. Therefore this mutant stimulus-responsive peptide may be more valuable for future protein engineering and bionanotechnology efforts.

Crystal structure of the TRIM25 B30.2 (PRYSPRY) domain: a key component of antiviral signalling.

PubMed

D'Cruz, Akshay A; Kershaw, Nadia J; Chiang, Jessica J; Wang, May K; Nicola, Nicos A; Babon, Jeffrey J; Gack, Michaela U; Nicholson, Sandra E

2013-12-01

TRIM (tripartite motif) proteins primarily function as ubiquitin E3 ligases that regulate the innate immune response to infection. TRIM25 [also known as Efp (oestrogen-responsive finger protein)] has been implicated in the regulation of oestrogen receptor α signalling and in the regulation of innate immune signalling via RIG-I (retinoic acid-inducible gene-I). RIG-I senses cytosolic viral RNA and is subsequently ubiquitinated by TRIM25 at its N-terminal CARDs (caspase recruitment domains), leading to type I interferon production. The interaction with RIG-I is dependent on the TRIM25 B30.2 domain, a protein-interaction domain composed of the PRY and SPRY tandem sequence motifs. In the present study we describe the 1.8 Å crystal structure of the TRIM25 B30.2 domain, which exhibits a typical B30.2/SPRY domain fold comprising two N-terminal α-helices, thirteen β-strands arranged into two β-sheets and loop regions of varying lengths. A comparison with other B30.2/SPRY structures and an analysis of the loop regions identified a putative binding pocket, which is likely to be involved in binding target proteins. This was supported by mutagenesis and functional analyses, which identified two key residues (Asp(488) and Trp(621)) in the TRIM25 B30.2 domain as being critical for binding to the RIG-I CARDs.

Crystal structure of the TRIM25 B30.2 (PRYSPRY) domain: a key component of antiviral signalling

PubMed Central

D'Cruz, Akshay A.; Kershaw, Nadia J.; Chiang, Jessica J.; Wang, May K.; Nicola, Nicos A.; Babon, Jeffrey J.; Gack, Michaela U.; Nicholson, Sandra E.

2014-01-01

TRIM (tripartite motif) proteins primarily function as ubiquitin E3 ligases that regulate the innate immune response to infection. TRIM25 [also known as Efp (oestrogen-responsive finger protein)] has been implicated in the regulation of oestrogen receptor α signalling and in the regulation of innate immune signalling via RIG-I (retinoic acid-inducible gene-I). RIG-I senses cytosolic viral RNA and is subsequently ubiquitinated by TRIM25 at its N-terminal CARDs (caspase recruitment domains), leading to type I interferon production. The interaction with RIG-I is dependent on the TRIM25 B30.2 domain, a protein-interaction domain composed of the PRY and SPRY tandem sequence motifs. In the present study we describe the 1.8 Å crystal structure of the TRIM25 B30.2 domain, which exhibits a typical B30.2/SPRY domain fold comprising two N-terminal α-helices, thirteen β-strands arranged into two β-sheets and loop regions of varying lengths. A comparison with other B30.2/SPRY structures and an analysis of the loop regions identified a putative binding pocket, which is likely to be involved in binding target proteins. This was supported by mutagenesis and functional analyses, which identified two key residues (Asp488 and Trp621) in the TRIM25 B30.2 domain as being critical for binding to the RIG-I CARDs. PMID:24015671

Alteration of the mode of antibacterial action of a defensin by the amino-terminal loop substitution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Bin; Zhu, Shunyi, E-mail: Zhusy@ioz.ac.cn

Highlights: Black-Right-Pointing-Pointer Al-M is an engineered fungal defensin with the n-loop of an insect defensin. Black-Right-Pointing-Pointer Al-M adopts a native defensin-like structure with high antibacterial potency. Black-Right-Pointing-Pointer Al-M kills bacteria through a membrane disruptive mechanism. Black-Right-Pointing-Pointer This work sheds light on the functional evolution of CS{alpha}{beta}-type defensins. -- Abstract: Ancient invertebrate-type and classical insect-type defensins (AITDs and CITDs) are two groups of evolutionarily related antimicrobial peptides (AMPs) that adopt a conserved cysteine-stabilized {alpha}-helical and {beta}-sheet (CS{alpha}{beta}) fold with a different amino-terminal loop (n-loop) size and diverse modes of antibacterial action. Although they both are identified as inhibitors of cell wallmore » biosynthesis, only CITDs evolved membrane disruptive ability by peptide oligomerization to form pores. To understand how this occurred, we modified micasin, a fungus-derived AITDs with a non-membrane disruptive mechanism, by substituting its n-loop with that of an insect-derived CITDs. After air oxidization, the synthetic hybrid defensin (termed Al-M) was structurally identified by circular dichroism (CD) and functionally evaluated by antibacterial and membrane permeability assays and electronic microscopic observation. Results showed that Al-M folded into a native-like defensin structure, as determined by its CD spectrum that is similar to that of micasin. Al-M was highly efficacious against the Gram-positive bacterium Bacillus megaterium with a lethal concentration of 1.76 {mu}M. As expected, in contrast to micasin, Al-M killed the bacteria through a membrane disruptive mechanism of action. The alteration in modes of action supports a key role of the n-loop extension in assembling functional surface of CITDs for membrane disruption. Our work provides mechanical evidence for evolutionary relationship between AITDs and CITDs.« less

HTL resummation in the light cone gauge

NASA Astrophysics Data System (ADS)

Chen, Qi; Hou, De-fu

2018-04-01

The light cone gauge with light cone variables is often used in pQCD calculations in relativistic heavy-ion collision physics. The Hard Thermal Loops (HTL) resummation is an indispensable technique for hot QCD calculation. It was developed in covariant gauges with conventional Minkowski varaiables; we shall extend this method to the light cone gauge. In the real time formalism, using the Mandelstam-Leibbrant prescription of (n·K)‑1, we calculate the transverse and longitudinal components of the gluon HTL self energy, and prove that there are no infrared divergences. With this HTL self energy, we derive the HTL resummed gluon propagator in the light cone gauge. We also calculate the quark HTL self energy and the resummed quark propagator in the light cone gauge and find it is gauge independent. As application examples, we analytically calculate the damping rates of hard quarks and gluons with the HTL resummed gluon propagator in the light cone gauge and showed that they are gauge independent. The final physical results are identical to those computed in covariant gauge, as they should be. Supported by National Natural Science Foundation of China (11375070, 11735007, 11521064)

The Bayesian reconstruction of the in-medium heavy quark potential from lattice QCD and its stability

NASA Astrophysics Data System (ADS)

Burnier, Yannis; Kaczmarek, Olaf; Rothkopf, Alexander

2016-01-01

We report recent results of a non-perturbative determination of the static heavy-quark potential in quenched and dynamical lattice QCD at finite temperature. The real and imaginary part of this complex quantity are extracted from the spectral function of Wilson line correlators in Coulomb gauge. To obtain spectral information from Euclidean time numerical data, our study relies on a novel Bayesian prescription that differs from the Maximum Entropy Method. We perform simulations on quenched 323 × Nτ (β = 7.0, ξ = 3.5) lattices with Nτ = 24, …, 96, which cover 839MeV ≥ T ≥ 210MeV. To investigate the potential in a quark-gluon plasma with light u,d and s quarks we utilize Nf = 2 + 1 ASQTAD lattices with ml = ms/20 by the HotQCD collaboration, giving access to temperatures between 286MeV ≥ T ≥ 148MeV. The real part of the potential exhibits a clean transition from a linear, confining behavior in the hadronic phase to a Debye screened form above deconfinement. Interestingly its values lie close to the color singlet free energies in Coulomb gauge at all temperatures. We estimate the imaginary part on quenched lattices and find that it is of the same order of magnitude as in hard-thermal loop perturbation theory. From among all the systematic checks carried out in our study, we discuss explicitly the dependence of the result on the default model and the number of datapoints.

ON THE STRENGTH OF THE HEMISPHERIC RULE AND THE ORIGIN OF ACTIVE-REGION HELICITY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Y.-M., E-mail: yi.wang@nrl.navy.mil

Vector magnetograph and morphological observations have shown that the solar magnetic field tends to have negative (positive) helicity in the northern (southern) hemisphere, although only ∼60%-70% of active regions appear to obey this 'hemispheric rule'. In contrast, at least ∼80% of quiescent filaments and filament channels that form during the decay of active regions follow the rule. We attribute this discrepancy to the difficulty in determining the helicity sign of newly emerged active regions, which are dominated by their current-free component; as the transverse field is canceled at the polarity inversion lines, however, the axial component becomes dominant there, allowingmore » a more reliable determination of the original active-region chirality. We thus deduce that the hemispheric rule is far stronger than generally assumed, and cannot be explained by stochastic processes. Earlier studies have shown that the twist associated with the axial tilt of active regions is too small to account for the observed helicity; here, both tilt and twist are induced by the Coriolis force acting on the diverging flow in the emerging flux tube. However, in addition to this east-west expansion about the apex of the loop, each of its legs must expand continually in cross section during its rise through the convection zone, thereby acquiring a further twist through the Coriolis force. Since this transverse pressure effect is not limited by drag or tension forces, the final twist depends mainly on the rise time, and may be large enough to explain the observed active-region helicity.« less

The alpha dynamo parameter and measurability of helicities in magnetohydrodynamic turbulence

NASA Technical Reports Server (NTRS)

Matthaeus, W. H.; Goldstein, M. L.; Lantz, S. R.

1986-01-01

Alpha, an important parameter in dynamo theory, is shown to be proportional to either the kinetic, current, magnetic, or velocity helicities of the fluctuating magnetic field and fluctuating velocity field. The particular helicity to which alpha is proportional depends on the assumptions used in deriving the first-order smoothed equations that describe the alpha effect. In two cases, viz., when alpha is proportional to either the magnetic helicity or velocity helicity, alpha can be determined experimentally from two-point measurements of the fluctuating fields in incompressible, homogeneous turbulence with arbitrary rotational symmetry. For the other two possibilities, alpha can be determined if the turbulence is isotropic.

Enhanced Control for Local Helicity Injection on the Pegasus ST

NASA Astrophysics Data System (ADS)

Pierren, C.; Bongard, M. W.; Fonck, R. J.; Lewicki, B. T.; Perry, J. M.

2017-10-01

Local helicity injection (LHI) experiments on Pegasus rely upon programmable control of a 250 MVA modular power supply system that drives the electromagnets and helicity injection systems. Precise control of the central solenoid is critical to experimental campaigns that test the LHI Taylor relaxation limit and the coupling efficiency of LHI-produced plasmas to Ohmic current drive. Enhancement and expansion of the present control system is underway using field programmable gate array (FPGA) technology for digital logic and control, coupled to new 10 MHz optical-to-digital transceivers for semiconductor level device communication. The system accepts optical command signals from existing analog feedback controllers, transmits them to multiple devices in parallel H-bridges, and aggregates their status signals for fault detection. Present device-level multiplexing/de-multiplexing and protection logic is extended to include bridge-level protections with the FPGA. An input command filter protects against erroneous and/or spurious noise generated commands that could otherwise cause device failures. Fault registration and response times with the FPGA system are 25 ns. Initial system testing indicates an increased immunity to power supply induced noise, enabling plasma operations at higher working capacitor bank voltage. This can increase the applied helicity injection drive voltage, enable longer pulse lengths and improve Ohmic loop voltage control. Work supported by US DOE Grant DE-FG02-96ER54375.

Asymptotics of QCD traveling waves with fluctuations and running coupling effects

NASA Astrophysics Data System (ADS)

Beuf, Guillaume

2008-09-01

Extending the Balitsky-Kovchegov (BK) equation independently to running coupling or to fluctuation effects due to pomeron loops is known to lead in both cases to qualitative changes of the traveling-wave asymptotic solutions. In this paper we study the extension of the forward BK equation, including both running coupling and fluctuations effects, extending the method developed for the fixed coupling case [E. Brunet, B. Derrida, A.H. Mueller, S. Munier, Phys. Rev. E 73 (2006) 056126, cond-mat/0512021]. We derive the exact asymptotic behavior in rapidity of the probabilistic distribution of the saturation scale.

Higher Order Heavy Quark Corrections to Deep-Inelastic Scattering

NASA Astrophysics Data System (ADS)

Blümlein, Johannes; DeFreitas, Abilio; Schneider, Carsten

2015-04-01

The 3-loop heavy flavor corrections to deep-inelastic scattering are essential for consistent next-to-next-to-leading order QCD analyses. We report on the present status of the calculation of these corrections at large virtualities Q2. We also describe a series of mathematical, computer-algebraic and combinatorial methods and special function spaces, needed to perform these calculations. Finally, we briefly discuss the status of measuring αs (MZ), the charm quark mass mc, and the parton distribution functions at next-to-next-to-leading order from the world precision data on deep-inelastic scattering.

Weak mixing below the weak scale in dark-matter direct detection

NASA Astrophysics Data System (ADS)

Brod, Joachim; Grinstein, Benjamin; Stamou, Emmanuel; Zupan, Jure

2018-02-01

If dark matter couples predominantly to the axial-vector currents with heavy quarks, the leading contribution to dark-matter scattering on nuclei is either due to one-loop weak corrections or due to the heavy-quark axial charges of the nucleons. We calculate the effects of Higgs and weak gauge-boson exchanges for dark matter coupling to heavy-quark axial-vector currents in an effective theory below the weak scale. By explicit computation, we show that the leading-logarithmic QCD corrections are important, and thus resum them to all orders using the renormalization group.

First moments of nucleon generalized parton distributions

DOE PAGES

Wang, P.; Thomas, A. W.

2010-06-01

We extrapolate the first moments of the generalized parton distributions using heavy baryon chiral perturbation theory. The calculation is based on the one loop level with the finite range regularization. The description of the lattice data is satisfactory, and the extrapolated moments at physical pion mass are consistent with the results obtained with dimensional regularization, although the extrapolation in the momentum transfer to t=0 does show sensitivity to form factor effects, which lie outside the realm of chiral perturbation theory. We discuss the significance of the results in the light of modern experiments as well as QCD inspired models.

Equilibrium Reconstruction on the Large Helical Device

DOE Office of Scientific and Technical Information (OSTI.GOV)

Samuel A. Lazerson, D. Gates, D. Monticello, H. Neilson, N. Pomphrey, A. Reiman S. Sakakibara, and Y. Suzuki

Equilibrium reconstruction is commonly applied to axisymmetric toroidal devices. Recent advances in computational power and equilibrium codes have allowed for reconstructions of three-dimensional fields in stellarators and heliotrons. We present the first reconstructions of finite beta discharges in the Large Helical Device (LHD). The plasma boundary and magnetic axis are constrained by the pressure profile from Thomson scattering. This results in a calculation of plasma beta without a-priori assumptions of the equipartition of energy between species. Saddle loop arrays place additional constraints on the equilibrium. These reconstruction utilize STELLOPT, which calls VMEC. The VMEC equilibrium code assumes good nested fluxmore » surfaces. Reconstructed magnetic fields are fed into the PIES code which relaxes this constraint allowing for the examination of the effect of islands and stochastic regions on the magnetic measurements.« less

Electroproduction of {eta} mesons in the S{sub 11}(1535) resonance region at high momentum transfer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dalton, M. M.; Adams, G. S.; Moziak, B.

2009-07-15

The differential cross section for the process p(e,e{sup '}p){eta} has been measured at Q{sup 2}{approx}5.7 and 7.0(GeV/c){sup 2} for center-of-mass energies from threshold to 1.8 GeV, encompassing the S{sub 11}(1535) resonance, which dominates the channel. This is the highest momentum-transfer measurement of this exclusive process to date. The helicity-conserving transition amplitude A{sub 1/2}, for the production of the S{sub 11}(1535) resonance, is extracted from the data. Within the limited Q{sup 2} now measured, this quantity appears to begin scaling as Q{sup -3}--a predicted, but not definitive, signal of the dominance of perturbative QCD at Q{sup 2}{approx}5 (GeV/c){sup 2}.

What is the right formalism to search for resonances?

NASA Astrophysics Data System (ADS)

Mikhasenko, M.; Pilloni, A.; Nys, J.; Albaladejo, M.; Fernández-Ramírez, C.; Jackura, A.; Mathieu, V.; Sherrill, N.; Skwarnicki, T.; Szczepaniak, A. P.

2018-03-01

Hadron decay chains constitute one of the main sources of information on the QCD spectrum. We discuss the differences between several partial wave analysis formalisms used in the literature to build the amplitudes. We match the helicity amplitudes to the covariant tensor basis. Hereby, we pay attention to the analytical properties of the amplitudes and separate singularities of kinematical and dynamical nature. We study the analytical properties of the spin-orbit (LS) formalism, and some of the covariant tensor approaches. In particular, we explicitly build the amplitudes for the B→ ψ π K and B→ \\bar{D}π π decays, and show that the energy dependence of the covariant approach is model dependent. We also show that the usual recursive construction of covariant tensors explicitly violates crossing symmetry, which would lead to different resonance parameters extracted from scattering and decay processes.

Mining protein loops using a structural alphabet and statistical exceptionality

PubMed Central

2010-01-01

Background Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. Results We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 Å). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of amino-acid conservation with at least four significant positions and 87% of long loops contain at least one such word. We complement our analysis with the detection of statistically over-represented patterns of structural letters as in conventional DNA sequence analysis. About 30% (930) of structural words are over-represented, and cover about 40% of loop lengths. Interestingly, these words exhibit lower structural variability and higher sequential specificity, suggesting structural or functional constraints. Conclusions We developed a method to systematically decompose and study protein loops using recurrent structural motifs. This method is based on the structural alphabet HMM-SA and not on structural alignment and geometrical parameters. We extracted meaningful structural motifs that are found in both short and long loops. To our knowledge, it is the first time that pattern mining helps to increase the signal-to-noise ratio in protein loops. This finding helps to better describe protein loops and might permit to decrease the complexity of long-loop analysis. Detailed results are available at http://www.mti.univ-paris-diderot.fr/publication/supplementary/2009/ACCLoop/. PMID:20132552

Mining protein loops using a structural alphabet and statistical exceptionality.

PubMed

Regad, Leslie; Martin, Juliette; Nuel, Gregory; Camproux, Anne-Claude

2010-02-04

Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 A). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of amino-acid conservation with at least four significant positions and 87% of long loops contain at least one such word. We complement our analysis with the detection of statistically over-represented patterns of structural letters as in conventional DNA sequence analysis. About 30% (930) of structural words are over-represented, and cover about 40% of loop lengths. Interestingly, these words exhibit lower structural variability and higher sequential specificity, suggesting structural or functional constraints. We developed a method to systematically decompose and study protein loops using recurrent structural motifs. This method is based on the structural alphabet HMM-SA and not on structural alignment and geometrical parameters. We extracted meaningful structural motifs that are found in both short and long loops. To our knowledge, it is the first time that pattern mining helps to increase the signal-to-noise ratio in protein loops. This finding helps to better describe protein loops and might permit to decrease the complexity of long-loop analysis. Detailed results are available at http://www.mti.univ-paris-diderot.fr/publication/supplementary/2009/ACCLoop/.

Current systems of coronal loops in 3D MHD simulations

NASA Astrophysics Data System (ADS)

Warnecke, J.; Chen, F.; Bingert, S.; Peter, H.

2017-11-01

Aims: We study the magnetic field and current structure associated with a coronal loop. Through this we investigate to what extent the assumptions of a force-free magnetic field break down and where they might be justified. Methods: We analyze a three-dimensional (3D) magnetohydrodynamic (MHD) model of the solar corona in an emerging active region with the focus on the structure of the forming coronal loops. The lower boundary of this simulation is taken from a model of an emerging active region. As a consequence of the emerging magnetic flux and the horizontal motions at the surface a coronal loop forms self-consistently. We investigate the current density along magnetic field lines inside (and outside) this loop and study the magnetic and plasma properties in and around this loop. The loop is defined as the bundle of field lines that coincides with enhanced emission in extreme UV. Results: We find that the total current along the emerging loop changes its sign from being antiparallel to parallel to the magnetic field. This is caused by the inclination of the loop together with the footpoint motion. Around the loop, the currents form a complex non-force-free helical structure. This is directly related to a bipolar current structure at the loop footpoints at the base of the corona and a local reduction of the background magnetic field (I.e., outside the loop) caused by the plasma flow into and along the loop. Furthermore, the locally reduced magnetic pressure in the loop allows the loop to sustain a higher density, which is crucial for the emission in extreme UV. The action of the flow on the magnetic field hosting the loop turns out to also be responsible for the observed squashing of the loop. Conclusions: The complex magnetic field and current system surrounding it can only be modeled in 3D MHD models where the magnetic field has to balance the plasma pressure. A one-dimensional coronal loop model or a force-free extrapolation cannot capture the current system and the complex interaction of the plasma and the magnetic field in the coronal loop, despite the fact that the loop is under low-β conditions.

QCD Sum Rules and Models for Generalized Parton Distributions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anatoly Radyushkin

2004-10-01

I use QCD sum rule ideas to construct models for generalized parton distributions. To this end, the perturbative parts of QCD sum rules for the pion and nucleon electromagnetic form factors are interpreted in terms of GPDs and two models are discussed. One of them takes the double Borel transform at adjusted value of the Borel parameter as a model for nonforward parton densities, and another is based on the local duality relation. Possible ways of improving these Ansaetze are briefly discussed.

Two-gluon and trigluon glueballs from dynamical holography QCD

NASA Astrophysics Data System (ADS)

Chen, Yi-dian; Huang, Mei

2016-12-01

We study the scalar, vector and tensor two-gluon and trigluon glueball spectra in the framework of the 5-dimension dynamical holographic QCD model, where the metric structure is deformed self-consistently by the dilaton field. For comparison, the glueball spectra are also calculated in the hard-wall and soft-wall holographic QCD models. In order to distinguish glueballs with even and odd parities, we introduce a positive and negative coupling between the dilaton field and glueballs, and for higher spin glueballs, we introduce a deformed 5-dimension mass. With this set-up, there is only one free parameter from the quadratic dilaton profile in the dynamical holographic QCD model, which is fixed by the scalar glueball spectra. It is found that the two-gluon glueball spectra produced in the dynamical holographic QCD model are in good agreement with lattice data. Among six trigluon glueballs, the produced masses for 1±- and 2-- are in good agreement with lattice data, and the produced masses for 0--, 0+- and 2+- are around 1.5 GeV lighter than lattice results. This result might indicate that the three trigluon glueballs of 0--, 0+- and 2+- are dominated by the three-gluon condensate contribution. Supported by the NSFC (11175251, 11621131001), DFG and NSFC (CRC 110), CAS Key Project KJCX2-EW-N01, K.C.Wong Education Foundation, and Youth Innovation Promotion Association of CAS

Magnetic design constraints of helical solenoids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lopes, M. L.; Krave, S. T.; Tompkins, J. C.

2015-01-30

Helical solenoids have been proposed as an option for a Helical Cooling Channel for muons in a proposed Muon Collider. Helical solenoids can provide the required three main field components: solenoidal, helical dipole, and a helical gradient. In general terms, the last two are a function of many geometric parameters: coil aperture, coil radial and longitudinal dimensions, helix period and orbit radius. In this paper, we present design studies of a Helical Solenoid, addressing the geometric tunability limits and auxiliary correction system.

A new approach to analytic, non-perturbative and gauge-invariant QCD

NASA Astrophysics Data System (ADS)

Fried, H. M.; Grandou, T.; Sheu, Y.-M.

2012-11-01

Following a previous calculation of quark scattering in eikonal approximation, this paper presents a new, analytic and rigorous approach to the calculation of QCD phenomena. In this formulation a basic distinction between the conventional "idealistic" description of QCD and a more "realistic" description is brought into focus by a non-perturbative, gauge-invariant evaluation of the Schwinger solution for the QCD generating functional in terms of the exact Fradkin representations of Green's functional G(x,y|A) and the vacuum functional L[A]. Because quarks exist asymptotically only in bound states, their transverse coordinates can never be measured with arbitrary precision; the non-perturbative neglect of this statement leads to obstructions that are easily corrected by invoking in the basic Lagrangian a probability amplitude which describes such transverse imprecision. The second result of this non-perturbative analysis is the appearance of a new and simplifying output called "Effective Locality", in which the interactions between quarks by the exchange of a "gluon bundle"-which "bundle" contains an infinite number of gluons, including cubic and quartic gluon interactions-display an exact locality property that reduces the several functional integrals of the formulation down to a set of ordinary integrals. It should be emphasized that "non-perturbative" here refers to the effective summation of all gluons between a pair of quark lines-which may be the same quark line, as in a self-energy graph-but does not (yet) include a summation over all closed-quark loops which are tied by gluon-bundle exchange to the rest of the "Bundle Diagram". As an example of the power of these methods we offer as a first analytic calculation the quark-antiquark binding potential of a pion, and the corresponding three-quark binding potential of a nucleon, obtained in a simple way from relevant eikonal scattering approximations. A second calculation, analytic, non-perturbative and gauge-invariant, of a nucleon-nucleon binding potential to form a model deuteron, will appear separately.

Amplitudes in the N=4 supersymmetric Yang-Mills theory from quantum geometry of momentum space

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gorsky, A.

We discuss multiloop maximally helicity violating amplitudes in the N=4 supersymmetric Yang-Mills theory in terms of effective gravity in the momentum space with IR regulator branes as degrees of freedom. Kinematical invariants of external particles yield the moduli spaces of complex or Kahler structures which are the playgrounds for the Kodaira-Spencer or Kahler type gravity. We suggest fermionic representation of the loop maximally helicity violating amplitudes in the N=4 supersymmetric Yang-Mills theory assuming the identification of the IR regulator branes with Kodaira-Spencer fermions in the B model and Lagrangian branes in the A model. The two-easy mass box diagram ismore » related to the correlator of fermionic currents on the spectral curve in the B model or hyperbolic volume in the A model and it plays the role of a building block in the whole picture. The Bern-Dixon-Smirnov-like ansatz has the interpretation as the semiclassical limit of a fermionic correlator. It is argued that fermionic representation implies a kind of integrability on the moduli spaces. We conjecture the interpretation of the reggeon degrees of freedom in terms of the open strings stretched between the IR regulator branes.« less

Posttranscriptional modifications in the A-loop of 23S rRNAs from selected archaea and eubacteria.

PubMed Central

Hansen, M A; Kirpekar, F; Ritterbusch, W; Vester, B

2002-01-01

Posttranscriptional modifications were mapped in helices 90-92 of 23S rRNA from the following phylogenetically diverse organisms: Haloarcula marismortui, Sulfolobus acidocaldarius, Bacillus subtilis, and Bacillus stearothermophilus. Helix 92 is a component of the ribosomal A-site, which contacts the aminoacyl-tRNA during protein synthesis, implying that posttranscriptional modifications in helices 90-92 may be important for ribosome function. RNA fragments were isolated from 23S rRNA by site-directed RNase H digestion. A novel method of mapping modifications by analysis of short, nucleotide-specific, RNase digestion fragments with Matrix Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS) was utilized. The MALDI-MS data were complemented by two primer extension techniques using reverse transcriptase. One technique utilizes decreasing concentrations of deoxynucleotide triphosphates to map 2'-O-ribose methylations. In the other, the rRNA is chemically modified, followed by mild alkaline hydrolysis to map pseudouridines (psis). A total of 10 posttranscriptionally methylated nucleotides and 6 psis were detected in the five organisms. Eight of the methylated nucleotides and one psi have not been reported previously. The distribution of modified nucleotides and their locations on the surface of the ribosomal peptidyl transferase cleft suggests functional importance. PMID:11911366

Proposed structure of putative glucose channel in GLUT1 facilitative glucose transporter.

PubMed Central

Zeng, H; Parthasarathy, R; Rampal, A L; Jung, C Y

1996-01-01

A family of structurally related intrinsic membrane proteins (facilitative glucose transporters) catalyzes the movement of glucose across the plasma membrane of animal cells. Evidence indicates that these proteins show a common structural motif where approximately 50% of the mass is embedded in lipid bilayer (transmembrane domain) in 12 alpha-helices (transmembrane helices; TMHs) and accommodates a water-filled channel for substrate passage (glucose channel) whose tertiary structure is currently unknown. Using recent advances in protein structure prediction algorithms we proposed here two three-dimensional structural models for the transmembrane glucose channel of GLUT1 glucose transporter. Our models emphasize the physical dimension and water accessibility of the channel, loop lengths between TMHs, the macrodipole orientation in four-helix bundle motif, and helix packing energy. Our models predict that five TMHs, either TMHs 3, 4, 7, 8, 11 (Model 1) or TMHs 2, 5, 11, 8, 7 (Model 2), line the channel, and the remaining TMHs surround these channel-lining TMHs. We discuss how our models are compatible with the experimental data obtained with this protein, and how they can be used in designing new biochemical and molecular biological experiments in elucidation of the structural basis of this important protein function. Images FIGURE 1 FIGURE 2 FIGURE 4 FIGURE 5 PMID:8770183

Probing the Interaction of Brain Fatty Acid Binding Protein (B-FABP) with Model Membranes

PubMed Central

Dyszy, Fábio; Pinto, Andressa P. A.; Araújo, Ana P. U.; Costa-Filho, Antonio J.

2013-01-01

Brain fatty acid-binding protein (B-FABP) interacts with biological membranes and delivers polyunsaturated fatty acids (FAs) via a collisional mechanism. The binding of FAs in the protein and the interaction with membranes involve a motif called “portal region”, formed by two small α-helices, A1 and A2, connected by a loop. We used a combination of site-directed mutagenesis and electron spin resonance to probe the changes in the protein and in the membrane model induced by their interaction. Spin labeled B-FABP mutants and lipidic spin probes incorporated into a membrane model confirmed that B-FABP interacts with micelles through the portal region and led to structural changes in the protein as well in the micelles. These changes were greater in the presence of LPG when compared to the LPC models. ESR spectra of B-FABP labeled mutants showed the presence of two groups of residues that responded to the presence of micelles in opposite ways. In the presence of lysophospholipids, group I of residues, whose side chains point outwards from the contact region between the helices, had their mobility decreased in an environment of lower polarity when compared to the same residues in solution. The second group, composed by residues with side chains situated at the interface between the α-helices, experienced an increase in mobility in the presence of the model membranes. These modifications in the ESR spectra of B-FABP mutants are compatible with a less ordered structure of the portal region inner residues (group II) that is likely to facilitate the delivery of FAs to target membranes. On the other hand, residues in group I and micelle components have their mobilities decreased probably as a result of the formation of a collisional complex. Our results bring new insights for the understanding of the gating and delivery mechanisms of FABPs. PMID:23555925

Unfolding of a ClC chloride transporter retains memory of its evolutionary history.

PubMed

Min, Duyoung; Jefferson, Robert E; Qi, Yifei; Wang, Jing Yang; Arbing, Mark A; Im, Wonpil; Bowie, James U

2018-05-01

ClC chloride channels and transporters are important for chloride homeostasis in species from bacteria to human. Mutations in ClC proteins cause genetically inherited diseases, some of which are likely to involve folding defects. The ClC proteins present a challenging and unusual biological folding problem because they are large membrane proteins possessing a complex architecture, with many reentrant helices that go only partway through membrane and loop back out. Here we were able to examine the unfolding of the Escherichia coli ClC transporter, ClC-ec1, using single-molecule forced unfolding methods. We found that the protein could be separated into two stable halves that unfolded independently. The independence of the two domains is consistent with an evolutionary model in which the two halves arose from independently folding subunits that later fused together. Maintaining smaller folding domains of lesser complexity within large membrane proteins may be an advantageous strategy to avoid misfolding traps.

Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler.

PubMed

Bindewald, Eckart; Grunewald, Calvin; Boyle, Brett; O'Connor, Mary; Shapiro, Bruce A

2008-10-01

One approach to designing RNA nanoscale structures is to use known RNA structural motifs such as junctions, kissing loops or bulges and to construct a molecular model by connecting these building blocks with helical struts. We previously developed an algorithm for detecting internal loops, junctions and kissing loops in RNA structures. Here we present algorithms for automating or assisting many of the steps that are involved in creating RNA structures from building blocks: (1) assembling building blocks into nanostructures using either a combinatorial search or constraint satisfaction; (2) optimizing RNA 3D ring structures to improve ring closure; (3) sequence optimisation; (4) creating a unique non-degenerate RNA topology descriptor. This effectively creates a computational pipeline for generating molecular models of RNA nanostructures and more specifically RNA ring structures with optimized sequences from RNA building blocks. We show several examples of how the algorithms can be utilized to generate RNA tecto-shapes.