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Sample records for densely-looped transciptionally-active chromatinfor

  1. SATB1 packages densely-looped, transciptionally-active chromatinfor coordinated expression of cytokine genes

    Energy Technology Data Exchange (ETDEWEB)

    Cai, Shutao; Lee, Charles C.; Kohwi-Shigematsu, Terumi

    2006-05-23

    SATB1 is an important regulator of nuclear architecture that anchors specialized DNA sequences onto its cage-like network and recruits chromatin remodeling/modifying factors to control gene transcription. We studied the role of SATB1 in regulating the coordinated expression of Il5, Il4, and Il13 from the 200kb cytokine gene cluster region of mouse chromosome 11 during T-helper 2 (Th2)-cell activation. We show that upon cell activation, SATB1 is rapidly induced to form a unique transcriptionally-active chromatin structure that includes the cytokine gene region. Chromatin is folded into numerous small loops all anchored by SATB1, is histone H3 acetylated at lysine 9/14, and associated with Th2-specific factors, GATA3, STAT6, c-Maf, the chromatin-remodeling enzyme Brg-1, and RNA polymerase II across the 200kb region. Before activation, the chromatin displays some of these features, such as association with GATA3 and STAT6, but these were insufficient for cytokine gene expression. Using RNA interference (RNAi), we show that upon cell activation, SATB1 is not only required for chromatin folding into dense loops, but also for c-Maf induction and subsequently for Il4, Il5, and Il13 transcription. Our results show that SATB1 is an important determinant for chromatin architecture that constitutes a novel higher-order, transcriptionally-active chromatin structure upon Th2-cell activation.

  2. Two-point boundary correlation functions of dense loop models

    Directory of Open Access Journals (Sweden)

    Alexi Morin-Duchesne, Jesper Lykke Jacobsen

    2018-06-01

    Full Text Available We investigate six types of two-point boundary correlation functions in the dense loop model. These are defined as ratios $Z/Z^0$ of partition functions on the $m\\times n$ square lattice, with the boundary condition for $Z$ depending on two points $x$ and $y$. We consider: the insertion of an isolated defect (a and a pair of defects (b in a Dirichlet boundary condition, the transition (c between Dirichlet and Neumann boundary conditions, and the connectivity of clusters (d, loops (e and boundary segments (f in a Neumann boundary condition. For the model of critical dense polymers, corresponding to a vanishing loop weight ($\\beta = 0$, we find determinant and pfaffian expressions for these correlators. We extract the conformal weights of the underlying conformal fields and find $\\Delta = -\\frac18$, $0$, $-\\frac3{32}$, $\\frac38$, $1$, $\\tfrac \\theta \\pi (1+\\tfrac{2\\theta}\\pi$, where $\\theta$ encodes the weight of one class of loops for the correlator of type f. These results are obtained by analysing the asymptotics of the exact expressions, and by using the Cardy-Peschel formula in the case where $x$ and $y$ are set to the corners. For type b, we find a $\\log|x-y|$ dependence from the asymptotics, and a $\\ln (\\ln n$ term in the corner free energy. This is consistent with the interpretation of the boundary condition of type b as the insertion of a logarithmic field belonging to a rank two Jordan cell. For the other values of $\\beta = 2 \\cos \\lambda$, we use the hypothesis of conformal invariance to predict the conformal weights and find $\\Delta = \\Delta_{1,2}$, $\\Delta_{1,3}$, $\\Delta_{0,\\frac12}$, $\\Delta_{1,0}$, $\\Delta_{1,-1}$ and $\\Delta_{\\frac{2\\theta}\\lambda+1,\\frac{2\\theta}\\lambda+1}$, extending the results of critical dense polymers. With the results for type f, we reproduce a Coulomb gas prediction for the valence bond entanglement entropy of Jacobsen and Saleur.

  3. Magnetic moment, vorticity-spin coupling and parity-odd conductivity of chiral fermions in 4-dimensional Wigner functions

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Jian-hua [Shandong Provincial Key Laboratory of Optical Astronomy and Solar-Terrestrial Environment, Institute of Space Sciences, Shandong University, Weihai, Shandong 264209 (China); Wang, Qun, E-mail: qunwang@ustc.edu.cn [Interdisciplinary Center for Theoretical Study and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Physics Department, Brookhaven National Laboratory, Upton, NY 11973-5000 (United States)

    2015-10-07

    We demonstrate the emergence of the magnetic moment and spin-vorticity coupling of chiral fermions in 4-dimensional Wigner functions. In linear response theory with space–time varying electromagnetic fields, the parity-odd part of the electric conductivity can also be derived which reproduces results of the one-loop and the hard-thermal or hard-dense loop. All these properties show that the 4-dimensional Wigner functions capture comprehensive aspects of physics for chiral fermions in electromagnetic fields.

  4. Magnetic moment, vorticity-spin coupling and parity-odd conductivity of chiral fermions in 4-dimensional Wigner functions

    Directory of Open Access Journals (Sweden)

    Jian-hua Gao

    2015-10-01

    Full Text Available We demonstrate the emergence of the magnetic moment and spin-vorticity coupling of chiral fermions in 4-dimensional Wigner functions. In linear response theory with space–time varying electromagnetic fields, the parity-odd part of the electric conductivity can also be derived which reproduces results of the one-loop and the hard-thermal or hard-dense loop. All these properties show that the 4-dimensional Wigner functions capture comprehensive aspects of physics for chiral fermions in electromagnetic fields.

  5. Power corrections to the HTL effective Lagrangian of QED

    Science.gov (United States)

    Carignano, Stefano; Manuel, Cristina; Soto, Joan

    2018-05-01

    We present compact expressions for the power corrections to the hard thermal loop (HTL) Lagrangian of QED in d space dimensions. These are corrections of order (L / T) 2, valid for momenta L ≪ T, where T is the temperature. In the limit d → 3 we achieve a consistent regularization of both infrared and ultraviolet divergences, which respects the gauge symmetry of the theory. Dimensional regularization also allows us to witness subtle cancellations of infrared divergences. We also discuss how to generalize our results in the presence of a chemical potential, so as to obtain the power corrections to the hard dense loop (HDL) Lagrangian.

  6. Medium effects in strange quark matter and strange stars

    International Nuclear Information System (INIS)

    Schertler, K.; Greiner, C.; Thoma, M.H.

    1997-01-01

    We investigate the properties of strange quark matter at zero temperature including medium effects. The quarks are considered as quasiparticles which acquire an effective mass generated by the interaction with the other quarks of the dense system. The effective quark masses are derived from the zero momentum limit of the dispersion relations following from an effective quark propagator obtained from resumming one-loop self-energy diagrams in the hard dense loop approximation. This leads to a thermodynamic self-consistent description of strange quark matter as an ideal Fermi gas of quasiparticles. Within this approach we find that medium effects reduce the overall binding energy with respect to 56 Fe of strange quark matter. For typical values of the strong coupling constant (α s >or∼1) strange quark matter is not absolutely stable. The application to pure strange quark matter stars shows that medium effects have, nevertheless, no impact on the mass-radius relation of the stars. However, a phase transition to hadronic matter at the surface of the stars becomes more likely. (orig.)

  7. AEKF-SLAM: A New Algorithm for Robotic Underwater Navigation

    Directory of Open Access Journals (Sweden)

    Xin Yuan

    2017-05-01

    Full Text Available In this work, we focus on key topics related to underwater Simultaneous Localization and Mapping (SLAM applications. Moreover, a detailed review of major studies in the literature and our proposed solutions for addressing the problem are presented. The main goal of this paper is the enhancement of the accuracy and robustness of the SLAM-based navigation problem for underwater robotics with low computational costs. Therefore, we present a new method called AEKF-SLAM that employs an Augmented Extended Kalman Filter (AEKF-based SLAM algorithm. The AEKF-based SLAM approach stores the robot poses and map landmarks in a single state vector, while estimating the state parameters via a recursive and iterative estimation-update process. Hereby, the prediction and update state (which exist as well in the conventional EKF are complemented by a newly proposed augmentation stage. Applied to underwater robot navigation, the AEKF-SLAM has been compared with the classic and popular FastSLAM 2.0 algorithm. Concerning the dense loop mapping and line mapping experiments, it shows much better performances in map management with respect to landmark addition and removal, which avoid the long-term accumulation of errors and clutters in the created map. Additionally, the underwater robot achieves more precise and efficient self-localization and a mapping of the surrounding landmarks with much lower processing times. Altogether, the presented AEKF-SLAM method achieves reliably map revisiting, and consistent map upgrading on loop closure.

  8. PROCEEDINGS OF RIKEN/BNL RESEARCH CENTER WORKSHOP, EQUILIBRIUM AND NON-EQUILIBRIM ASPECTS OF HOT, DENSE QCD, VOLUME 28.

    Energy Technology Data Exchange (ETDEWEB)

    De Vega, H.J.; Boyanovsky, D. [and others

    2000-07-17

    The Relativistic Heavy Ion Collider (RHIC) at Brookhaven, beginning operation this year, and the Large Hadron Collider (LHC) at CERN, beginning operation {approximately}2005, will provide an unprecedented range of energies and luminosities that will allow us to probe the Gluon-Quark plasma. At RHIC and LHC, at central rapidity typical estimates of energy densities and temperatures are e * 1-10 GeV/fm3 and T0 * 300 - 900 MeV. Such energies are well above current estimates for the GQ plasma. Initially, this hot, dense plasma is far from local thermal equilibrium, making the theoretical study of transport phenomena, kinetic and chemical equilibration in dense and hot plasmas, and related issues a matter of fundamental importance. During the last few years a consistent framework to study collective effects in the Gluon-Quark plasma, and a microscopic description of transport in terms of the hard thermal (and dense) loops resummation program has emerged. This approach has the potential of providing a microscopic formulation of transport, in the regime of temperatures and densities to be achieved at RHIC and LHC. A parallel development over the last few years has provided a consistent formulation of non-equilibrium quantum field theory that provides a real-time description of phenomena out of equilibrium. Novel techniques including non-perturbative approaches and the dynamical renormalization group techniques lead to new insights into transport and relaxation. A deeper understanding of collective.excitations and transport phenomena in the GQ plasma could lead to recognize novel potential experimental signatures. New insights into small-c physics reveals a striking similarity between small-c and hard thermal loops, and novel real-time numerical simulations have recently studied the parton distributions and their thermalizations in the initial stages of a heavy ion collision.

  9. PROCEEDINGS OF RIKEN/BNL RESEARCH CENTER WORKSHOP, EQUILIBRIUM AND NON-EQUILIBRIM ASPECTTS OF HOT, DENSE QCD, VOLUME 28.

    Energy Technology Data Exchange (ETDEWEB)

    DE VEGA,H.J.; BOYANOVSKY,D. [and others

    2000-07-17

    The Relativistic Heavy Ion Collider (RHIC) at Brookhaven, beginning operation this year, and the Large Hadron Collider (LHC) at CERN, beginning operation {approximately}2005, will provide an unprecedented range of energies and luminosities that will allow us to probe the Gluon-Quark plasma. At RHIC and LHC, at central rapidity typical estimates of energy densities and temperatures are e * 1-10 GeV/fm3 and T0 * 300 - 900 MeV. Such energies are well above current estimates for the GQ plasma. Initially, this hot, dense plasma is far from local thermal equilibrium, making the theoretical study of transport phenomena, kinetic and chemical equilibration in dense and hot plasmas, and related issues a matter of fundamental importance. During the last few years a consistent framework to study collective effects in the Gluon-Quark plasma, and a microscopic description of transport in terms of the hard thermal (and dense) loops resummation program has emerged. This approach has the potential of providing a microscopic formulation of transport, in the regime of temperatures and densities to be achieved at RHIC and LHC. A parallel development over the last few years has provided a consistent formulation of non-equilibrium quantum field theory that provides a real-time description of phenomena out of equilibrium. Novel techniques including non-perturbative approaches and the dynamical renormalization group techniques lead to new insights into transport and relaxation. A deeper understanding of collective.excitations and transport phenomena in the GQ plasma could lead to recognize novel potential experimental signatures. New insights into small-c physics reveals a striking similarity between small-c and hard thermal loops, and novel real-time numerical simulations have recently studied the parton distributions and their thermalizations in the initial stages of a heavy ion collision.

  10. Sensitivity of coronal loop sausage mode frequencies and decay rates to radial and longitudinal density inhomogeneities: a spectral approach

    Science.gov (United States)

    Cally, Paul S.; Xiong, Ming

    2018-01-01

    Fast sausage modes in solar magnetic coronal loops are only fully contained in unrealistically short dense loops. Otherwise they are leaky, losing energy to their surrounds as outgoing waves. This causes any oscillation to decay exponentially in time. Simultaneous observations of both period and decay rate therefore reveal the eigenfrequency of the observed mode, and potentially insight into the tubes’ nonuniform internal structure. In this article, a global spectral description of the oscillations is presented that results in an implicit matrix eigenvalue equation where the eigenvalues are associated predominantly with the diagonal terms of the matrix. The off-diagonal terms vanish identically if the tube is uniform. A linearized perturbation approach, applied with respect to a uniform reference model, is developed that makes the eigenvalues explicit. The implicit eigenvalue problem is easily solved numerically though, and it is shown that knowledge of the real and imaginary parts of the eigenfrequency is sufficient to determine the width and density contrast of a boundary layer over which the tubes’ enhanced internal densities drop to ambient values. Linearized density kernels are developed that show sensitivity only to the extreme outside of the loops for radial fundamental modes, especially for small density enhancements, with no sensitivity to the core. Higher radial harmonics do show some internal sensitivity, but these will be more difficult to observe. Only kink modes are sensitive to the tube centres. Variation in internal and external Alfvén speed along the loop is shown to have little effect on the fundamental dimensionless eigenfrequency, though the associated eigenfunction becomes more compact at the loop apex as stratification increases, or may even displace from the apex.

  11. INJECTION OF PLASMA INTO THE NASCENT SOLAR WIND VIA RECONNECTION DRIVEN BY SUPERGRANULAR ADVECTION

    International Nuclear Information System (INIS)

    Yang Liping; He Jiansen; Tu Chuanyi; Chen Wenlei; Zhang Lei; Wang Linghua; Yan Limei; Peter, Hardi; Marsch, Eckart; Feng, Xueshang

    2013-01-01

    To understand the origin of the solar wind is one of the key research topics in modern solar and heliospheric physics. Previous solar wind models assumed that plasma flows outward along a steady magnetic flux tube that reaches continuously from the photosphere through the chromosphere into the corona. Inspired by more recent comprehensive observations, Tu et al. suggested a new scenario for the origin of the solar wind, in which it flows out in a magnetically open coronal funnel and mass is provided to the funnel by small-scale side loops. Thus mass is supplied by means of magnetic reconnection that is driven by supergranular convection. To validate this scenario and simulate the processes involved, a 2.5 dimensional (2.5D) numerical MHD model is established in the present paper. In our simulation a closed loop moves toward an open funnel, which has opposite polarity and is located at the edge of a supergranulation cell, and magnetic reconnection is triggered and continues while gradually opening up one half of the closed loop. Its other half connects with the root of the open funnel and forms a new closed loop which is submerged by a reconnection plasma stream flowing downward. Thus we find that the outflowing plasma in the newly reconnected funnel originates not only from the upward reconnection flow but also from the high-pressure leg of the originally closed loop. This implies an efficient supply of mass from the dense loop to the dilute funnel. The mass flux of the outflow released from the funnel considered in our study is calculated to be appropriate for providing the mass flux at the coronal base of the solar wind, though additional heating and acceleration mechanisms are necessary to keep the velocity at the higher location. Our numerical model demonstrates that in the funnel the mass for the solar wind may be supplied from adjacent closed loops via magnetic reconnection as well as directly from the footpoints of open funnels.

  12. Enthalpy-Based Thermal Evolution of Loops: II. Improvements to the Model

    Science.gov (United States)

    Cargill, P. J.; Bradshaw, S. J.; Klimchuk, J. A.

    2011-01-01

    This paper further develops the zero-dimensional (0D) hydrodynamic coronal loop model "Enthalpy-based Thermal Evolution of Loops" (EBTEL) originally proposed by Klimchuk et al (2008), which studies the plasma response to evolving coronal heating. It has typically been applied to impulsive heating events. The basis of EBTEL is the modelling of mass exchange between the corona and transition region and chromosphere in response to heating variations, with the key parameter being the ratio of transition region to coronal radiation. We develop new models for this parameter that now include gravitational stratification and a physically motivated approach to radiative cooling. A number of examples are presented, including nanoflares in short and long loops, and a small flare. It is found that while the evolution of the loop temperature is rather insensitive to the details of the model, accurate tracking of the density requires the inclusion of our new features. In particular, we are able to now obtain highly over-dense loops in the late cooling phase and decreases to the coronal density arising due to stratification. The 0D results are compared to a 1D hydro code (Hydrad). The agreement is acceptable, with the exception of the flare case where some versions of Hydrad can give significantly lower densities. This is attributed to the method used to model the chromosphere in a flare. EBTEL is suitable for general use as a tool for (a) quick-look results of loop evolution in response to a given heating function and (b) situations where the modelling of hundreds or thousands of elemental loops is needed. A single run takes a few seconds on a contemporary laptop.

  13. Proceedings of RIKEN BNL research center workshop, equilibrium and non-equilibrium aspects of hot, dense QCD, Vol. 28

    International Nuclear Information System (INIS)

    De Vega, H.J.; Boyanovsky, D.

    2000-01-01

    The Relativistic Heavy Ion Collider (RHIC) at Brookhaven, beginning operation this year, and the Large Hadron Collider (LHC) at CERN, beginning operation ∼2005, will provide an unprecedented range of energies and luminosities that will allow us to probe the Gluon-Quark plasma. At RHIC and LHC, at central rapidity typical estimates of energy densities and temperatures are e * 1-10 GeV/fm3 and T0 * 300 - 900 MeV. Such energies are well above current estimates for the GQ plasma. Initially, this hot, dense plasma is far from local thermal equilibrium, making the theoretical study of transport phenomena, kinetic and chemical equilibration in dense and hot plasmas, and related issues a matter of fundamental importance. During the last few years a consistent framework to study collective effects in the Gluon-Quark plasma, and a microscopic description of transport in terms of the hard thermal (and dense) loops resummation program has emerged. This approach has the potential of providing a microscopic formulation of transport, in the regime of temperatures and densities to be achieved at RHIC and LHC. A parallel development over the last few years has provided a consistent formulation of non-equilibrium quantum field theory that provides a real-time description of phenomena out of equilibrium. Novel techniques including non-perturbative approaches and the dynamical renormalization group techniques lead to new insights into transport and relaxation. A deeper understanding of collective.excitations and transport phenomena in the GQ plasma could lead to recognize novel potential experimental signatures. New insights into small-c physics reveals a striking similarity between small-c and hard thermal loops, and novel real-time numerical simulations have recently studied the parton distributions and their thermalizations in the initial stages of a heavy ion collision