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Sample records for random-phase approximation rpa

  1. Tensor hypercontracted ppRPA: Reducing the cost of the particle-particle random phase approximation from O(r 6) to O(r 4)

    International Nuclear Information System (INIS)

    Shenvi, Neil; Yang, Yang; Yang, Weitao; Aggelen, Helen van

    2014-01-01

    In recent years, interest in the random-phase approximation (RPA) has grown rapidly. At the same time, tensor hypercontraction has emerged as an intriguing method to reduce the computational cost of electronic structure algorithms. In this paper, we combine the particle-particle random phase approximation with tensor hypercontraction to produce the tensor-hypercontracted particle-particle RPA (THC-ppRPA) algorithm. Unlike previous implementations of ppRPA which scale as O(r 6 ), the THC-ppRPA algorithm scales asymptotically as only O(r 4 ), albeit with a much larger prefactor than the traditional algorithm. We apply THC-ppRPA to several model systems and show that it yields the same results as traditional ppRPA to within mH accuracy. Our method opens the door to the development of post-Kohn Sham functionals based on ppRPA without the excessive asymptotic cost of traditional ppRPA implementations

  2. SANS [small-angle neutron scattering] evaluation of the RPA [random phase approximation] theory for binary homopolymer mixtures

    International Nuclear Information System (INIS)

    Bates, F.S.; Koehler, W.C.; Wignall, G.D.; Fetters, L.J.

    1986-12-01

    A well characterized binary mixture of normal (protonated) and perdeuterated monodisperse 1,2 polybutenes has been studied by small-angle neutron scattering (SANS). For scattering wavevectors q greater than the inverse radius-of-gyration R/sub g/ -1 , the SANS intensity is quantitatively predicted by the random phase approximation (RPA) theory of deGennes over all measured values of the segment-segment interaction parameter Chi. In the region (Chi s-Chi)Chi s -1 > 0.5 the interaction parameter determined using the RPA theory for q > R/sub g/ -1 is greater than that calculated from the zero-angle intensity based on an Ornstein-Zernike plot, where Chi s represents the limit of single phase stability. These findings indicate a correlation between the critical fluctuation length ξ and R/sub g/ which is not accounted for by the RPA theory

  3. Tensor hypercontracted ppRPA: Reducing the cost of the particle-particle random phase approximation from O(r {sup 6}) to O(r {sup 4})

    Energy Technology Data Exchange (ETDEWEB)

    Shenvi, Neil; Yang, Yang; Yang, Weitao [Department of Chemistry, Duke University, Durham, NC 27708 (United States); Aggelen, Helen van [Department of Chemistry, Princeton University, Princeton, New Jersey 08544 (United States)

    2014-07-14

    In recent years, interest in the random-phase approximation (RPA) has grown rapidly. At the same time, tensor hypercontraction has emerged as an intriguing method to reduce the computational cost of electronic structure algorithms. In this paper, we combine the particle-particle random phase approximation with tensor hypercontraction to produce the tensor-hypercontracted particle-particle RPA (THC-ppRPA) algorithm. Unlike previous implementations of ppRPA which scale as O(r{sup 6}), the THC-ppRPA algorithm scales asymptotically as only O(r{sup 4}), albeit with a much larger prefactor than the traditional algorithm. We apply THC-ppRPA to several model systems and show that it yields the same results as traditional ppRPA to within mH accuracy. Our method opens the door to the development of post-Kohn Sham functionals based on ppRPA without the excessive asymptotic cost of traditional ppRPA implementations.

  4. Beyond the random phase approximation

    DEFF Research Database (Denmark)

    Olsen, Thomas; Thygesen, Kristian S.

    2013-01-01

    We assess the performance of a recently proposed renormalized adiabatic local density approximation (rALDA) for ab initio calculations of electronic correlation energies in solids and molecules. The method is an extension of the random phase approximation (RPA) derived from time-dependent density...... functional theory and the adiabatic connection fluctuation-dissipation theorem and contains no fitted parameters. The new kernel is shown to preserve the accurate description of dispersive interactions from RPA while significantly improving the description of short-range correlation in molecules, insulators......, and metals. For molecular atomization energies, the rALDA is a factor of 7 better than RPA and a factor of 4 better than the Perdew-Burke-Ernzerhof (PBE) functional when compared to experiments, and a factor of 3 (1.5) better than RPA (PBE) for cohesive energies of solids. For transition metals...

  5. The random phase approximation

    International Nuclear Information System (INIS)

    Schuck, P.

    1985-01-01

    RPA is the adequate theory to describe vibrations of the nucleus of very small amplitudes. These vibrations can either be forced by an external electromagnetic field or can be eigenmodes of the nucleus. In a one dimensional analogue the potential corresponding to such eigenmodes of very small amplitude should be rather stiff otherwise the motion risks to be a large amplitude one and to enter a region where the approximation is not valid. This means that nuclei which are supposedly well described by RPA must have a very stable groundstate configuration (must e.g. be very stiff against deformation). This is usually the case for doubly magic nuclei or close to magic nuclei which are in the middle of proton and neutron shells which develop a very stable groundstate deformation; we take the deformation as an example but there are many other possible degrees of freedom as, for example, compression modes, isovector degrees of freedom, spin degrees of freedom, and many more

  6. Static correlation beyond the random phase approximation

    DEFF Research Database (Denmark)

    Olsen, Thomas; Thygesen, Kristian Sommer

    2014-01-01

    derived from Hedin's equations (Random Phase Approximation (RPA), Time-dependent Hartree-Fock (TDHF), Bethe-Salpeter equation (BSE), and Time-Dependent GW) all reproduce the correct dissociation limit. We also show that the BSE improves the correlation energies obtained within RPA and TDHF significantly...... and confirms that BSE greatly improves the RPA and TDHF results despite the fact that the BSE excitation spectrum breaks down in the dissociation limit. In contrast, second order screened exchange gives a poor description of the dissociation limit, which can be attributed to the fact that it cannot be derived...

  7. Random phase approximation in relativistic approach

    International Nuclear Information System (INIS)

    Ma Zhongyu; Yang Ding; Tian Yuan; Cao Ligang

    2009-01-01

    Some special issues of the random phase approximation(RPA) in the relativistic approach are reviewed. A full consistency and proper treatment of coupling to the continuum are responsible for the successful application of the RPA in the description of dynamical properties of finite nuclei. The fully consistent relativistic RPA(RRPA) requires that the relativistic mean filed (RMF) wave function of the nucleus and the RRPA correlations are calculated in a same effective Lagrangian and the consistent treatment of the Dirac sea of negative energy states. The proper treatment of the single particle continuum with scattering asymptotic conditions in the RMF and RRPA is discussed. The full continuum spectrum can be described by the single particle Green's function and the relativistic continuum RPA is established. A separable form of the paring force is introduced in the relativistic quasi-particle RPA. (authors)

  8. Random-phase approximation and broken symmetry

    International Nuclear Information System (INIS)

    Davis, E.D.; Heiss, W.D.

    1986-01-01

    The validity of the random-phase approximation (RPA) in broken-symmetry bases is tested in an appropriate many-body system for which exact solutions are available. Initially the regions of stability of the self-consistent quasiparticle bases in this system are established and depicted in a 'phase' diagram. It is found that only stable bases can be used in an RPA calculation. This is particularly true for those RPA modes which are not associated with the onset of instability of the basis; it is seen that these modes do not describe any excited state when the basis is unstable, although from a formal point of view they remain acceptable. The RPA does well in a stable broken-symmetry basis provided one is not too close to a point where a phase transition occurs. This is true for both energies and matrix elements. (author)

  9. Modified random phase approximation for multipole excitations at finite temperature

    International Nuclear Information System (INIS)

    Nguyen Dinh Dang

    1991-01-01

    The modified finite temperature random phase approximation (modified FT-RPA) has been constructed with taking the influence of thermostat on the structure of quansiparticles into account. The modified FT-RPA linear response for electric quadrupole (λ π = 2 + ) and octupole (λ π = 3 - ) excitations in 5 8Ni has been calculated as a function of the nuclear temperature. As compared to the conventional FT-RPA the modified FT-RPA has given a stronger spreading for the strength distribution of quandrupole excitations at finite temperature T ≤ 3MeV. (author). 22 refs; 4 figs; 2 tabs

  10. Derivation of the RPA (Random Phase Approximation) Equation of ATDDFT (Adiabatic Time Dependent Density Functional Ground State Response Theory) from an Excited State Variational Approach Based on the Ground State Functional.

    Science.gov (United States)

    Ziegler, Tom; Krykunov, Mykhaylo; Autschbach, Jochen

    2014-09-09

    The random phase approximation (RPA) equation of adiabatic time dependent density functional ground state response theory (ATDDFT) has been used extensively in studies of excited states. It extracts information about excited states from frequency dependent ground state response properties and avoids, thus, in an elegant way, direct Kohn-Sham calculations on excited states in accordance with the status of DFT as a ground state theory. Thus, excitation energies can be found as resonance poles of frequency dependent ground state polarizability from the eigenvalues of the RPA equation. ATDDFT is approximate in that it makes use of a frequency independent energy kernel derived from the ground state functional. It is shown in this study that one can derive the RPA equation of ATDDFT from a purely variational approach in which stationary states above the ground state are located using our constricted variational DFT (CV-DFT) method and the ground state functional. Thus, locating stationary states above the ground state due to one-electron excitations with a ground state functional is completely equivalent to solving the RPA equation of TDDFT employing the same functional. The present study is an extension of a previous work in which we demonstrated the equivalence between ATDDFT and CV-DFT within the Tamm-Dancoff approximation.

  11. Variational random phase approximation for the anharmonic oscillator

    International Nuclear Information System (INIS)

    Dukelsky, J.; Schuck, P.

    1990-04-01

    The recently derived Variational Random Phase Approximation is examined using the anharmonic oscillator model. Special attention is paid to the ground state RPA wave function and the convergence of the proposed truncation scheme to obtain the diagonal density matrix. Comparison with the standard Coupled Cluster method is made

  12. Communication: Random phase approximation renormalized many-body perturbation theory

    International Nuclear Information System (INIS)

    Bates, Jefferson E.; Furche, Filipp

    2013-01-01

    We derive a renormalized many-body perturbation theory (MBPT) starting from the random phase approximation (RPA). This RPA-renormalized perturbation theory extends the scope of single-reference MBPT methods to small-gap systems without significantly increasing the computational cost. The leading correction to RPA, termed the approximate exchange kernel (AXK), substantially improves upon RPA atomization energies and ionization potentials without affecting other properties such as barrier heights where RPA is already accurate. Thus, AXK is more balanced than second-order screened exchange [A. Grüneis et al., J. Chem. Phys. 131, 154115 (2009)], which tends to overcorrect RPA for systems with stronger static correlation. Similarly, AXK avoids the divergence of second-order Møller-Plesset (MP2) theory for small gap systems and delivers a much more consistent performance than MP2 across the periodic table at comparable cost. RPA+AXK thus is an accurate, non-empirical, and robust tool to assess and improve semi-local density functional theory for a wide range of systems previously inaccessible to first-principles electronic structure calculations

  13. Random phase approximation: from Giant to Intra-doublet resonances

    International Nuclear Information System (INIS)

    Amusia, M.Ya.

    2004-01-01

    We discuss here the history and current achievements of one of the most powerful approaches of 20th century physics--the random phase approximation (RPA) that permits us to study collective or multiparticle effects in atoms, nuclei, molecules and clusters, as well as in quantum liquids. We concentrate on RPA application to studies of isolated atoms where it permits one to disclose the collective multielectron nature of so-called Giant resonances and predict a number of others, like Interference and Intra-doublet resonances. We present general theory as well as results of concrete calculations for a number of atoms

  14. Random phase approximation: from Giant to Intra-doublet resonances

    Energy Technology Data Exchange (ETDEWEB)

    Amusia, M.Ya. E-mail: amusia@vms.huji.ac.il

    2004-06-01

    We discuss here the history and current achievements of one of the most powerful approaches of 20th century physics--the random phase approximation (RPA) that permits us to study collective or multiparticle effects in atoms, nuclei, molecules and clusters, as well as in quantum liquids. We concentrate on RPA application to studies of isolated atoms where it permits one to disclose the collective multielectron nature of so-called Giant resonances and predict a number of others, like Interference and Intra-doublet resonances. We present general theory as well as results of concrete calculations for a number of atoms.

  15. Beyond the Random Phase Approximation for the Electron Correlation Energy: The Importance of Single Excitations

    OpenAIRE

    Ren, Xinguo; Rinke, Patrick; Tkatchenko, Alexandre; Scheffler, Matthias

    2010-01-01

    The random-phase approximation (RPA) for the electron correlation energy, combined with the exact-exchange (EX) energy, represents the state-of-the-art exchange-correlation functional within density-functional theory. However, the standard RPA practice-evaluating both the EX and the RPA correlation energies using Kohn-Sham (KS) orbitals from local or semilocal exchange-correlation functionals-leads to a systematic underbinding of molecules and solids. Here we demonstrate that this behavior ca...

  16. Quasilinear theory without the random phase approximation

    International Nuclear Information System (INIS)

    Weibel, E.S.; Vaclavik, J.

    1980-08-01

    The system of quasilinear equations is derived without making use of the random phase approximation. The fluctuating quantities are described by the autocorrelation function of the electric field using the techniques of Fourier analysis. The resulting equations posses the necessary conservation properties, but comprise new terms which hitherto have been lost in the conventional derivations

  17. Relativistic continuum random phase approximation in spherical nuclei

    International Nuclear Information System (INIS)

    Daoutidis, Ioannis

    2009-01-01

    Covariant density functional theory is used to analyze the nuclear response in the external multipole fields. The investigations are based on modern functionals with zero range and density dependent coupling constants. After a self-consistent solution of the Relativistic Mean Field (RMF) equations for the nuclear ground states multipole giant resonances are studied within the Relativistic Random Phase Approximation (RRPA), the small amplitude limit of the time-dependent RMF. The coupling to the continuum is treated precisely by calculating the single particle Greens-function of the corresponding Dirac equation. In conventional methods based on a discretization of the continuum this was not possible. The residual interaction is derived from the same RMF Lagrangian. This guarantees current conservation and a precise decoupling of the Goldstone modes. For nuclei with open shells pairing correlations are taken into account in the framework of BCS theory and relativistic quasiparticle RPA. Continuum RPA (CRPA) presents a robust method connected with an astonishing reduction of the numerical effort as compared to conventional methods. Modes of various multipolarities and isospin are investigated, in particular also the newly discovered Pygmy modes in the vicinity of the neutron evaporation threshold. The results are compared with conventional discrete RPA calculations as well as with experimental data. We find that the full treatment of the continuum is essential for light nuclei and the study of resonances in the neighborhood of the threshold. (orig.)

  18. Relativistic continuum random phase approximation in spherical nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Daoutidis, Ioannis

    2009-10-01

    Covariant density functional theory is used to analyze the nuclear response in the external multipole fields. The investigations are based on modern functionals with zero range and density dependent coupling constants. After a self-consistent solution of the Relativistic Mean Field (RMF) equations for the nuclear ground states multipole giant resonances are studied within the Relativistic Random Phase Approximation (RRPA), the small amplitude limit of the time-dependent RMF. The coupling to the continuum is treated precisely by calculating the single particle Greens-function of the corresponding Dirac equation. In conventional methods based on a discretization of the continuum this was not possible. The residual interaction is derived from the same RMF Lagrangian. This guarantees current conservation and a precise decoupling of the Goldstone modes. For nuclei with open shells pairing correlations are taken into account in the framework of BCS theory and relativistic quasiparticle RPA. Continuum RPA (CRPA) presents a robust method connected with an astonishing reduction of the numerical effort as compared to conventional methods. Modes of various multipolarities and isospin are investigated, in particular also the newly discovered Pygmy modes in the vicinity of the neutron evaporation threshold. The results are compared with conventional discrete RPA calculations as well as with experimental data. We find that the full treatment of the continuum is essential for light nuclei and the study of resonances in the neighborhood of the threshold. (orig.)

  19. Random phase approximation applied to solids, molecules, and graphene-metal interfaces

    DEFF Research Database (Denmark)

    Olsen, Thomas; Thygesen, Kristian S.

    2013-01-01

    The random phase approximation (RPA) is attracting renewed interest as a universal and accurate method for first-principles total energy calculations. The RPA naturally accounts for long-range dispersive forces without compromising accuracy for short-range interactions making the RPA superior...... to semilocal and hybrid functionals in systems dominated by weak van der Waals or mixed covalent-dispersive interactions. In this work, we present plane-wave-based RPA calculations for a broad collection of systems with bond types ranging from strong covalent to van der Waals. Our main result is the RPA...... the RPA captures both the weak covalent and dispersive forces, which are equally important for these systems. We benchmark our implementation in the GPAW electronic structure code by calculating cohesive energies of graphite and a range of covalently bonded solids and molecules as well as the dissociation...

  20. Extending the random-phase approximation for electronic correlation energies: the renormalized adiabatic local density approximation

    DEFF Research Database (Denmark)

    Olsen, Thomas; Thygesen, Kristian S.

    2012-01-01

    The adiabatic connection fluctuation-dissipation theorem with the random phase approximation (RPA) has recently been applied with success to obtain correlation energies of a variety of chemical and solid state systems. The main merit of this approach is the improved description of dispersive forces...... while chemical bond strengths and absolute correlation energies are systematically underestimated. In this work we extend the RPA by including a parameter-free renormalized version of the adiabatic local-density (ALDA) exchange-correlation kernel. The renormalization consists of a (local) truncation...... of the ALDA kernel for wave vectors q > 2kF, which is found to yield excellent results for the homogeneous electron gas. In addition, the kernel significantly improves both the absolute correlation energies and atomization energies of small molecules over RPA and ALDA. The renormalization can...

  1. Restricted second random phase approximations and Tamm-Dancoff approximations for electronic excitation energy calculations

    International Nuclear Information System (INIS)

    Peng, Degao; Yang, Yang; Zhang, Peng; Yang, Weitao

    2014-01-01

    In this article, we develop systematically second random phase approximations (RPA) and Tamm-Dancoff approximations (TDA) of particle-hole and particle-particle channels for calculating molecular excitation energies. The second particle-hole RPA/TDA can capture double excitations missed by the particle-hole RPA/TDA and time-dependent density-functional theory (TDDFT), while the second particle-particle RPA/TDA recovers non-highest-occupied-molecular-orbital excitations missed by the particle-particle RPA/TDA. With proper orbital restrictions, these restricted second RPAs and TDAs have a formal scaling of only O(N 4 ). The restricted versions of second RPAs and TDAs are tested with various small molecules to show some positive results. Data suggest that the restricted second particle-hole TDA (r2ph-TDA) has the best overall performance with a correlation coefficient similar to TDDFT, but with a larger negative bias. The negative bias of the r2ph-TDA may be induced by the unaccounted ground state correlation energy to be investigated further. Overall, the r2ph-TDA is recommended to study systems with both single and some low-lying double excitations with a moderate accuracy. Some expressions on excited state property evaluations, such as 〈S ^2 〉 are also developed and tested

  2. Restricted second random phase approximations and Tamm-Dancoff approximations for electronic excitation energy calculations

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Degao; Yang, Yang; Zhang, Peng [Department of Chemistry, Duke University, Durham, North Carolina 27708 (United States); Yang, Weitao, E-mail: weitao.yang@duke.edu [Department of Chemistry and Department of Physics, Duke University, Durham, North Carolina 27708 (United States)

    2014-12-07

    In this article, we develop systematically second random phase approximations (RPA) and Tamm-Dancoff approximations (TDA) of particle-hole and particle-particle channels for calculating molecular excitation energies. The second particle-hole RPA/TDA can capture double excitations missed by the particle-hole RPA/TDA and time-dependent density-functional theory (TDDFT), while the second particle-particle RPA/TDA recovers non-highest-occupied-molecular-orbital excitations missed by the particle-particle RPA/TDA. With proper orbital restrictions, these restricted second RPAs and TDAs have a formal scaling of only O(N{sup 4}). The restricted versions of second RPAs and TDAs are tested with various small molecules to show some positive results. Data suggest that the restricted second particle-hole TDA (r2ph-TDA) has the best overall performance with a correlation coefficient similar to TDDFT, but with a larger negative bias. The negative bias of the r2ph-TDA may be induced by the unaccounted ground state correlation energy to be investigated further. Overall, the r2ph-TDA is recommended to study systems with both single and some low-lying double excitations with a moderate accuracy. Some expressions on excited state property evaluations, such as 〈S{sup ^2}〉 are also developed and tested.

  3. Calculation of thermodynamic properties using the random-phase approximation: alpha-N2

    NARCIS (Netherlands)

    Jansen, A.P.J.; Schoorl, R.

    1988-01-01

    The random-phase approximation (RPA) for molecular crystals is extended in order to calculate thermodynamic properties. A recursion formula for thermodynamic averages of products of mean-field excitation and deexcitation operators is derived. With this formula the thermodynamic average of any

  4. Beyond the random-phase approximation for the electron correlation energy: the importance of single excitations.

    Science.gov (United States)

    Ren, Xinguo; Tkatchenko, Alexandre; Rinke, Patrick; Scheffler, Matthias

    2011-04-15

    The random-phase approximation (RPA) for the electron correlation energy, combined with the exact-exchange (EX) energy, represents the state-of-the-art exchange-correlation functional within density-functional theory. However, the standard RPA practice--evaluating both the EX and the RPA correlation energies using Kohn-Sham (KS) orbitals from local or semilocal exchange-correlation functionals--leads to a systematic underbinding of molecules and solids. Here we demonstrate that this behavior can be corrected by adding a "single excitation" contribution, so far not included in the standard RPA scheme. A similar improvement can also be achieved by replacing the non-self-consistent EX total energy by the corresponding self-consistent Hartree-Fock total energy, while retaining the RPA correlation energy evaluated using KS orbitals. Both schemes achieve chemical accuracy for a standard benchmark set of noncovalent intermolecular interactions.

  5. Toward a consistent random phase approximation based on the relativistic Hartree approximation

    International Nuclear Information System (INIS)

    Price, C.E.; Rost, E.; Shepard, J.R.; McNeil, J.A.

    1992-01-01

    We examine the random phase approximation (RPA) based on a relativistic Hartree approximation description for nuclear ground states. This model includes contributions from the negative energy sea at the one-loop level. We emphasize consistency between the treatment of the ground state and the RPA. This consistency is important in the description of low-lying collective levels but less important for the longitudinal (e,e') quasielastic response. We also study the effect of imposing a three-momentum cutoff on negative energy sea contributions. A cutoff of twice the nucleon mass improves agreement with observed spin-orbit splittings in nuclei compared to the standard infinite cutoff results, an effect traceable to the fact that imposing the cutoff reduces m * /m. Consistency is much more important than the cutoff in the description of low-lying collective levels. The cutoff model also provides excellent agreement with quasielastic (e,e') data

  6. Collective nuclear excitations with Skyrme-second random-phase approximation

    International Nuclear Information System (INIS)

    Gambacurta, D.; Catara, F.; Grasso, M.

    2010-01-01

    Second random-phase approximation (RPA) calculations with a Skyrme force are performed to describe both high- and low-lying excited states in 16 O. The coupling between one particle-one hole and two particle-two hole as well as that between two particle-two hole configurations among themselves are fully taken into account, and the residual interaction is never neglected; we do not resort therefore to a generally used approximate scheme where only the first kind of coupling is considered. The issue of the rearrangement terms in the matrix elements beyond the standard RPA will be considered in detail in a forthcoming paper. Two approximations are employed here for these rearrangement terms: they are either neglected or evaluated with the RPA procedure. As a general feature of second RPA results, a several-MeV shift of the strength distribution to lower energies is systematically found with respect to RPA distributions. A much more important fragmentation of the strength is also naturally provided by the second RPA owing to the huge number of two particle-two hole configurations. A better description of the excitation energies of the low-lying 0 + and 2 + states is obtained with the second RPA than with the RPA.

  7. Application of the resonating Hartree-Fock random phase approximation to the Lipkin model

    International Nuclear Information System (INIS)

    Nishiyama, S.; Ishida, K.; Ido, M.

    1996-01-01

    We have applied the resonating Hartree-Fock (Res-HF) approximation to the exactly solvable Lipkin model by utilizing a newly developed orbital-optimization algorithm. The Res-HF wave function was superposed by two Slater determinants (S-dets) which give two corresponding local energy minima of monopole ''deformations''. The self-consistent Res-HF calculation gives an excellent ground-state correlation energy. There exist excitations due to small vibrational fluctuations of the orbitals and mixing coefficients around their stationary values. They are described by a new approximation called the resonating Hartree-Fock random phase approximation (Res-HF RPA). Matrices of the second-order variation of the Res-HF energy have the same structures as those of the Res-HF RPA's matrices. The quadratic steepest descent of the Res-HF energy in the orbital optimization is considered to include certainly both effects of RPA-type fluctuations up to higher orders and their mode-mode couplings. It is a very important and interesting task to apply the Res-HF RPA to the Lipkin model with the use of the stationary values and to prove the above argument. It turns out that the Res-HF RPA works far better than the usual HF RPA and the renormalized one. We also show some important features of the Res-HF RPA. (orig.)

  8. Dispersive and Covalent Interactions between Graphene and Metal Surfaces from the Random Phase Approximation

    DEFF Research Database (Denmark)

    Olsen, Thomas; Yan, Jun; Mortensen, Jens Jørgen

    2011-01-01

    We calculate the potential energy surfaces for graphene adsorbed on Cu(111), Ni(111), and Co(0001) using density functional theory and the random phase approximation (RPA). For these adsorption systems covalent and dispersive interactions are equally important and while commonly used approximations...... for exchange-correlation functionals give inadequate descriptions of either van der Waals or chemical bonds, RPA accounts accurately for both. It is found that the adsorption is a delicate competition between a weak chemisorption minimum close to the surface and a physisorption minimum further from the surface....

  9. Scattering in particle-hole space: simple approximations to nuclear RPA calculations in the continuum

    International Nuclear Information System (INIS)

    Toledo Piza, A.F.R. de.

    1987-01-01

    The Random Phase Approximation (RPA) treatment of nuclear small amplitude vibrations including particle-hole continua is handled in terms of previously developed techniques to treat single-particle resonances in a reaction theoretical framework. A hierarchy of interpretable approximations is derived and a simple working approximation is proposed which involves a numerical effort no larger than that involved in standard, discrete RPA calculations. (Author) [pt

  10. Correlated random-phase approximation from densities and in-medium matrix elements

    Energy Technology Data Exchange (ETDEWEB)

    Trippel, Richard; Roth, Robert [Institut fuer Kernphysik, Technische Universitaet Darmstadt (Germany)

    2016-07-01

    The random-phase approximation (RPA) as well as the second RPA (SRPA) are established tools for the study of collective excitations in nuclei. Addressing the well known lack of correlations, we derived a universal framework for a fully correlated RPA based on the use of one- and two-body densities. We apply densities from coupled cluster theory and investigate the impact of correlations. As an alternative approach to correlations we use matrix elements transformed via in-medium similarity renormalization group (IM-SRG) in combination with RPA and SRPA. We find that within SRPA the use of IM-SRG matrix elements leads to the disappearance of instabilities of low-lying states. For the calculations we use normal-ordered two- plus three-body interactions derived from chiral effective field theory. We apply different Hamiltonians to a number of doubly-magic nuclei and calculate electric transition strengths.

  11. Random-phase approximation and its extension for the O(2) anharmonic oscillator

    International Nuclear Information System (INIS)

    Aouissat, Z.; Martin, C.

    2004-01-01

    We apply the random-phase approximation (RPA) and its extension called renormalized RPA to the quantum anharmonic oscillator with an O(2) symmetry. We first obtain the equation for the RPA frequencies in the standard and in the renormalized RPAs using the equation-of-motion method. In the case where the ground state has a broken symmetry, we check the existence of a zero frequency in the standard and in the renormalized RPAs. Then we use a time-dependent approach where the standard-RPA frequencies are obtained as small oscillations around the static solution in the time-dependent Hartree-Bogolyubov equation. We draw the parallel between the two approaches. (orig.)

  12. Large-Scale Cubic-Scaling Random Phase Approximation Correlation Energy Calculations Using a Gaussian Basis.

    Science.gov (United States)

    Wilhelm, Jan; Seewald, Patrick; Del Ben, Mauro; Hutter, Jürg

    2016-12-13

    We present an algorithm for computing the correlation energy in the random phase approximation (RPA) in a Gaussian basis requiring [Formula: see text] operations and [Formula: see text] memory. The method is based on the resolution of the identity (RI) with the overlap metric, a reformulation of RI-RPA in the Gaussian basis, imaginary time, and imaginary frequency integration techniques, and the use of sparse linear algebra. Additional memory reduction without extra computations can be achieved by an iterative scheme that overcomes the memory bottleneck of canonical RPA implementations. We report a massively parallel implementation that is the key for the application to large systems. Finally, cubic-scaling RPA is applied to a thousand water molecules using a correlation-consistent triple-ζ quality basis.

  13. Random-phase approximation and its extension for the O(2) anharmonic oscillator

    Energy Technology Data Exchange (ETDEWEB)

    Aouissat, Z. [Institut fuer Kernphysik, Technische Hochschule Darmstadt, Schlossgarten 9, D-64289, Darmstadt (Germany); Martin, C. [Groupe de Physique Theorique, Institut de Physique Nucleaire, F-91406, Orsay Cedex (France)

    2004-02-01

    We apply the random-phase approximation (RPA) and its extension called renormalized RPA to the quantum anharmonic oscillator with an O(2) symmetry. We first obtain the equation for the RPA frequencies in the standard and in the renormalized RPAs using the equation-of-motion method. In the case where the ground state has a broken symmetry, we check the existence of a zero frequency in the standard and in the renormalized RPAs. Then we use a time-dependent approach where the standard-RPA frequencies are obtained as small oscillations around the static solution in the time-dependent Hartree-Bogolyubov equation. We draw the parallel between the two approaches. (orig.)

  14. Accurate Quasiparticle Spectra from the T-Matrix Self-Energy and the Particle-Particle Random Phase Approximation.

    Science.gov (United States)

    Zhang, Du; Su, Neil Qiang; Yang, Weitao

    2017-07-20

    The GW self-energy, especially G 0 W 0 based on the particle-hole random phase approximation (phRPA), is widely used to study quasiparticle (QP) energies. Motivated by the desirable features of the particle-particle (pp) RPA compared to the conventional phRPA, we explore the pp counterpart of GW, that is, the T-matrix self-energy, formulated with the eigenvectors and eigenvalues of the ppRPA matrix. We demonstrate the accuracy of the T-matrix method for molecular QP energies, highlighting the importance of the pp channel for calculating QP spectra.

  15. Benchmark tests and spin adaptation for the particle-particle random phase approximation

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Yang; Steinmann, Stephan N.; Peng, Degao [Department of Chemistry, Duke University, Durham, North Carolina 27708 (United States); Aggelen, Helen van, E-mail: Helen.VanAggelen@UGent.be [Department of Chemistry, Duke University, Durham, North Carolina 27708 (United States); Department of Inorganic and Physical Chemistry, Ghent University, 9000 Ghent (Belgium); Yang, Weitao, E-mail: Weitao.Yang@duke.edu [Department of Chemistry and Department of Physics, Duke University, Durham, North Carolina 27708 (United States)

    2013-11-07

    The particle-particle random phase approximation (pp-RPA) provides an approximation to the correlation energy in density functional theory via the adiabatic connection [H. van Aggelen, Y. Yang, and W. Yang, Phys. Rev. A 88, 030501 (2013)]. It has virtually no delocalization error nor static correlation error for single-bond systems. However, with its formal O(N{sup 6}) scaling, the pp-RPA is computationally expensive. In this paper, we implement a spin-separated and spin-adapted pp-RPA algorithm, which reduces the computational cost by a substantial factor. We then perform benchmark tests on the G2/97 enthalpies of formation database, DBH24 reaction barrier database, and four test sets for non-bonded interactions (HB6/04, CT7/04, DI6/04, and WI9/04). For the G2/97 database, the pp-RPA gives a significantly smaller mean absolute error (8.3 kcal/mol) than the direct particle-hole RPA (ph-RPA) (22.7 kcal/mol). Furthermore, the error in the pp-RPA is nearly constant with the number of atoms in a molecule, while the error in the ph-RPA increases. For chemical reactions involving typical organic closed-shell molecules, pp- and ph-RPA both give accurate reaction energies. Similarly, both RPAs perform well for reaction barriers and nonbonded interactions. These results suggest that the pp-RPA gives reliable energies in chemical applications. The adiabatic connection formalism based on pairing matrix fluctuation is therefore expected to lead to widely applicable and accurate density functionals.

  16. Reference Determinant Dependence of the Random Phase Approximation in 3d Transition Metal Chemistry.

    Science.gov (United States)

    Bates, J E; Mezei, P D; Csonka, G I; Sun, J; Ruzsinszky, A

    2017-01-10

    Without extensive fitting, accurate prediction of transition metal chemistry is a challenge for semilocal and hybrid density funcitonals. The Random Phase Approximation (RPA) has been shown to yield superior results to semilocal functionals for main group thermochemistry, but much less is known about its performance for transition metals. We have therefore analyzed the behavior of reaction energies, barrier heights, and ligand dissociation energies obtained with RPA and compare our results to several semilocal and hybrid functionals. Particular attention is paid to the reference determinant dependence of RPA. We find that typically the results do not vary much between semilocal or hybrid functionals as a reference, as long as the fraction of exact exchange (EXX) mixing in the hybrid functional is small. For large fractions of EXX mixing, however, the Hartree-Fock-like nature of the determinant can severely degrade the performance. Overall, RPA systematically reduces the errors of semilocal functionals and delivers excellent performance from a single reference determinant for inherently multireference reactions. The behavior of dual hybrids that combine RPA correlation with a hybrid exchange energy was also explored, but ultimately did not lead to a systematic improvement compared to traditional RPA for these systems. We rationalize this conclusion by decomposing the contributions to the reaction energies, and briefly discuss the possible implications for double-hybrid functionals based on RPA. The correlation between EXX mixing and spin-symmetry breaking is also discussed.

  17. Assessment of correlation energies based on the random-phase approximation

    International Nuclear Information System (INIS)

    Paier, Joachim; Ren, Xinguo; Rinke, Patrick; Scheffler, Matthias; Scuseria, Gustavo E; Grüneis, Andreas; Kresse, Georg

    2012-01-01

    The random-phase approximation to the ground state correlation energy (RPA) in combination with exact exchange (EX) has brought the Kohn-Sham (KS) density functional theory one step closer towards a universal, ‘general purpose first-principles method’. In an effort to systematically assess the influence of several correlation energy contributions beyond RPA, this paper presents dissociation energies of small molecules and solids, activation energies for hydrogen transfer and non-hydrogen transfer reactions, as well as reaction energies for a number of common test sets. We benchmark EX + RPA and several flavors of energy functionals going beyond it: second-order screened exchange (SOSEX), single-excitation (SE) corrections, renormalized single-excitation (rSE) corrections and their combinations. Both the SE correction and the SOSEX contribution to the correlation energy significantly improve on the notorious tendency of EX + RPA to underbind. Surprisingly, activation energies obtained using EX + RPA based on a KS reference alone are remarkably accurate. RPA + SOSEX + rSE provides an equal level of accuracy for reaction as well as activation energies and overall gives the most balanced performance, because of which it can be applied to a wide range of systems and chemical reactions. (paper)

  18. Collapse of the random-phase approximation: Examples and counter-examples from the shell model

    International Nuclear Information System (INIS)

    Johnson, Calvin W.; Stetcu, Ionel

    2009-01-01

    The Hartree-Fock approximation to the many-fermion problem can break exact symmetries, and in some cases by changing a parameter in the interaction one can drive the Hartree-Fock minimum from a symmetry-breaking state to a symmetry-conserving state (also referred to as a 'phase transition' in the literature). The order of the transition is important when one applies the random-phase approximation (RPA) to the of the Hartree-Fock wave function: if first order, RPA is stable through the transition, but if second-order, then the RPA amplitudes become large and lead to unphysical results. The latter is known as 'collapse' of the RPA. While the difference between first- and second-order transitions in the RPA was first pointed out by Thouless, we present for the first time nontrivial examples of both first- and second-order transitions in a uniform model, the interacting shell-model, where we can compare to exact numerical results.

  19. Roles of antinucleon degrees of freedom in the relativistic random phase approximation

    Science.gov (United States)

    Kurasawa, Haruki; Suzuki, Toshio

    2015-11-01

    The roles of antinucleon degrees of freedom in the relativistic random phase approximation (RPA) are investigated. The energy-weighted sum of the RPA transition strengths is expressed in terms of the double commutator between the excitation operator and the Hamiltonian, as in nonrelativistic models. The commutator, however, should not be calculated in the usual way in the local field theory, because, otherwise, the sum vanishes. The sum value obtained correctly from the commutator is infinite, owing to the Dirac sea. Most of the previous calculations take into account only some of the nucleon-antinucleon states, in order to avoid divergence problems. As a result, RPA states with negative excitation energy appear, which make the sum value vanish. Moreover, disregarding the divergence changes the sign of nuclear interactions in the RPA equation that describes the coupling of the nucleon particle-hole states with the nucleon-antinucleon states. Indeed, the excitation energies of the spurious state and giant monopole states in the no-sea approximation are dominated by these unphysical changes. The baryon current conservation can be described without touching the divergence problems. A schematic model with separable interactions is presented, which makes the structure of the relativistic RPA transparent.

  20. Approximated calculation of the vacuum wave function and vacuum energy of the LGT with RPA method

    International Nuclear Information System (INIS)

    Hui Ping

    2004-01-01

    The coupled cluster method is improved with the random phase approximation (RPA) to calculate vacuum wave function and vacuum energy of 2 + 1 - D SU(2) lattice gauge theory. In this calculating, the trial wave function composes of single-hollow graphs. The calculated results of vacuum wave functions show very good scaling behaviors at weak coupling region l/g 2 >1.2 from the third order to the sixth order, and the vacuum energy obtained with RPA method is lower than the vacuum energy obtained without RPA method, which means that this method is a more efficient one

  1. Insight into organic reactions from the direct random phase approximation and its corrections

    Energy Technology Data Exchange (ETDEWEB)

    Ruzsinszky, Adrienn [Department of Physics, Temple University, Philadelphia, Pennsylvania 19122 (United States); Zhang, Igor Ying; Scheffler, Matthias [Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin (Germany)

    2015-10-14

    The performance of the random phase approximation (RPA) and beyond-RPA approximations for the treatment of electron correlation is benchmarked on three different molecular test sets. The test sets are chosen to represent three typical sources of error which can contribute to the failure of most density functional approximations in chemical reactions. The first test set (atomization and n-homodesmotic reactions) offers a gradually increasing balance of error from the chemical environment. The second test set (Diels-Alder reaction cycloaddition = DARC) reflects more the effect of weak dispersion interactions in chemical reactions. Finally, the third test set (self-interaction error 11 = SIE11) represents reactions which are exposed to noticeable self-interaction errors. This work seeks to answer whether any one of the many-body approximations considered here successfully addresses all these challenges.

  2. Insight into organic reactions from the direct random phase approximation and its corrections

    International Nuclear Information System (INIS)

    Ruzsinszky, Adrienn; Zhang, Igor Ying; Scheffler, Matthias

    2015-01-01

    The performance of the random phase approximation (RPA) and beyond-RPA approximations for the treatment of electron correlation is benchmarked on three different molecular test sets. The test sets are chosen to represent three typical sources of error which can contribute to the failure of most density functional approximations in chemical reactions. The first test set (atomization and n-homodesmotic reactions) offers a gradually increasing balance of error from the chemical environment. The second test set (Diels-Alder reaction cycloaddition = DARC) reflects more the effect of weak dispersion interactions in chemical reactions. Finally, the third test set (self-interaction error 11 = SIE11) represents reactions which are exposed to noticeable self-interaction errors. This work seeks to answer whether any one of the many-body approximations considered here successfully addresses all these challenges

  3. Exchange-correlation energy from pairing matrix fluctuation and the particle-particle random phase approximation.

    Science.gov (United States)

    van Aggelen, Helen; Yang, Yang; Yang, Weitao

    2014-05-14

    Despite their unmatched success for many applications, commonly used local, semi-local, and hybrid density functionals still face challenges when it comes to describing long-range interactions, static correlation, and electron delocalization. Density functionals of both the occupied and virtual orbitals are able to address these problems. The particle-hole (ph-) Random Phase Approximation (RPA), a functional of occupied and virtual orbitals, has recently known a revival within the density functional theory community. Following up on an idea introduced in our recent communication [H. van Aggelen, Y. Yang, and W. Yang, Phys. Rev. A 88, 030501 (2013)], we formulate more general adiabatic connections for the correlation energy in terms of pairing matrix fluctuations described by the particle-particle (pp-) propagator. With numerical examples of the pp-RPA, the lowest-order approximation to the pp-propagator, we illustrate the potential of density functional approximations based on pairing matrix fluctuations. The pp-RPA is size-extensive, self-interaction free, fully anti-symmetric, describes the strong static correlation limit in H2, and eliminates delocalization errors in H2(+) and other single-bond systems. It gives surprisingly good non-bonded interaction energies--competitive with the ph-RPA--with the correct R(-6) asymptotic decay as a function of the separation R, which we argue is mainly attributable to its correct second-order energy term. While the pp-RPA tends to underestimate absolute correlation energies, it gives good relative energies: much better atomization energies than the ph-RPA, as it has no tendency to underbind, and reaction energies of similar quality. The adiabatic connection in terms of pairing matrix fluctuation paves the way for promising new density functional approximations.

  4. Exchange-correlation energy from pairing matrix fluctuation and the particle-particle random phase approximation

    International Nuclear Information System (INIS)

    Aggelen, Helen van; Yang, Yang; Yang, Weitao

    2014-01-01

    Despite their unmatched success for many applications, commonly used local, semi-local, and hybrid density functionals still face challenges when it comes to describing long-range interactions, static correlation, and electron delocalization. Density functionals of both the occupied and virtual orbitals are able to address these problems. The particle-hole (ph-) Random Phase Approximation (RPA), a functional of occupied and virtual orbitals, has recently known a revival within the density functional theory community. Following up on an idea introduced in our recent communication [H. van Aggelen, Y. Yang, and W. Yang, Phys. Rev. A 88, 030501 (2013)], we formulate more general adiabatic connections for the correlation energy in terms of pairing matrix fluctuations described by the particle-particle (pp-) propagator. With numerical examples of the pp-RPA, the lowest-order approximation to the pp-propagator, we illustrate the potential of density functional approximations based on pairing matrix fluctuations. The pp-RPA is size-extensive, self-interaction free, fully anti-symmetric, describes the strong static correlation limit in H 2 , and eliminates delocalization errors in H 2 + and other single-bond systems. It gives surprisingly good non-bonded interaction energies – competitive with the ph-RPA – with the correct R −6 asymptotic decay as a function of the separation R, which we argue is mainly attributable to its correct second-order energy term. While the pp-RPA tends to underestimate absolute correlation energies, it gives good relative energies: much better atomization energies than the ph-RPA, as it has no tendency to underbind, and reaction energies of similar quality. The adiabatic connection in terms of pairing matrix fluctuation paves the way for promising new density functional approximations

  5. Application of the random phase approximation to complex problems in materials science

    International Nuclear Information System (INIS)

    Schimka, L.

    2012-01-01

    This thesis is devoted to the assessment and application of the random phase approximation (RPA) in the adiabatic-connection fluctuation-dissipation (ACFD) framework in solid state physics. The first part presents a review of density functional theory (DFT) and the ACFD theorem in the RPA. This includes an introduction to the many-body problem as well as a description of the implementation of the RPA in the Vienna Ab-initio Simulation Package (VASP). In the results part, the quality of the RPA is assessed and its performance compared to three (beyond) DFT functionals. The experimental values are corrected for the effect of phonon zero-point vibrational energies which were calculated at the DFT level from ab-initio. We find that the RPA describes all bonding situations very accurately, making it a promising candidate for more complex problems in solid state physics. In light of these findings, we investigate the carbon-water interaction in two specific cases: the adsorption of water on benzene and the adsorption of water on a graphene layer. We compare our results to a different correlated method: diffusion Monte Carlo (DMC). We find very good agreement and thus believe that our values can serve as a benchmark for the development of other DFT functionals to treat water-carbon interfaces. The highlight of this thesis is the successful application of the RPA to the long-standing and (at DFT level) unsolved CO adsorption puzzle. We show results for CO adsorption on Cu, late 4d metals and Pt. RPA is at present the only ab-initio method that describes adsorption and surface energies accurately at the same time and predicts the correct adsorption site in every single case. (author) [de

  6. Dielectric Matrix Formulation of Correlation Energies in the Random Phase Approximation: Inclusion of Exchange Effects.

    Science.gov (United States)

    Mussard, Bastien; Rocca, Dario; Jansen, Georg; Ángyán, János G

    2016-05-10

    Starting from the general expression for the ground state correlation energy in the adiabatic-connection fluctuation-dissipation theorem (ACFDT) framework, it is shown that the dielectric matrix formulation, which is usually applied to calculate the direct random phase approximation (dRPA) correlation energy, can be used for alternative RPA expressions including exchange effects. Within this famework, the ACFDT analog of the second order screened exchange (SOSEX) approximation leads to a logarithmic formula for the correlation energy similar to the direct RPA expression. Alternatively, the contribution of the exchange can be included in the kernel used to evaluate the response functions. In this case, the use of an approximate kernel is crucial to simplify the formalism and to obtain a correlation energy in logarithmic form. Technical details of the implementation of these methods are discussed, and it is shown that one can take advantage of density fitting or Cholesky decomposition techniques to improve the computational efficiency; a discussion on the numerical quadrature made on the frequency variable is also provided. A series of test calculations on atomic correlation energies and molecular reaction energies shows that exchange effects are instrumental for improvement over direct RPA results.

  7. Self-consistent Random Phase Approximation applied to a schematic model of the field theory

    International Nuclear Information System (INIS)

    Bertrand, Thierry

    1998-01-01

    The self-consistent Random Phase Approximation (SCRPA) is a method allowing in the mean-field theory inclusion of the correlations in the ground and excited states. It has the advantage of not violating the Pauli principle in contrast to RPA, that is based on the quasi-bosonic approximation; in addition, numerous applications in different domains of physics, show a possible variational character. However, the latter should be formally demonstrated. The first model studied with SCRPA is the anharmonic oscillator in the region where one of its symmetries is spontaneously broken. The ground state energy is reproduced by SCRPA more accurately than RPA, with no violation of the Ritz variational principle, what is not the case for the latter approximation. The success of SCRPA is the the same in case of ground state energy for a model mixing bosons and fermions. At the transition point the SCRPA is correcting RPA drastically, but far from this region the correction becomes negligible, both methods being of similar precision. In the deformed region in the case of RPA a spurious mode occurred due to the microscopical character of the model.. The SCRPA may also reproduce this mode very accurately and actually it coincides with an excitation in the exact spectrum

  8. Application of the random phase approximation to some atoms with ns2 ground state configurations

    International Nuclear Information System (INIS)

    Wright, L.A.

    1975-01-01

    Atomic bound state properties such as excitation energies and oscillator strengths were calculated by the Random Phase Approximation (RPA), also known as the Time Dependent Hartree-Fock Approximation (TDHFA). The RPA is equivalent to describing excited states as the creation of particle-hole pairs and the application to atoms is important for two reasons: the wide range of densities in an atom will cause the physical interpretation and mathematical approximations to be much different than with a uniform density system, such as an electron gas; this method could detect the existence of collective states in atoms similar to those responsible for the giant dipole resonances in nuclei. The method is shown to be superior to the H-F method in three basic ways: (1) The RPA contains explicit correlations between the excited and ground states. These are not included in the H-F theory. One can apply this method to large atoms since only these correlations are explicitly included. (2) The RPA calculates excitation energies directly without recourse to highly correlated ground state wavefunctions. This is in contrast to the method of configuration mixing which is known to have slow convergence properties. (3) Oscillator strengths and photoionization cross sections can be calculated by finding the eigenvectors corresponding excitation energy eigenvalues. The strength of the RPA is that the excitation energies and oscillator strengths, which are relative quantities, are calculated directly. The results for the oscillator strengths show an improvement of up to 45 percent over the H-F values and an improvement over the RPA done with Hartree wavefunctions by as much as 65 percent. The work was limited to atoms with an ns 2 ground state configuration. These atoms were He, Be, Mg and Ca

  9. Collective excitations in the Penson-Kolb model: A generalized random-phase-approximation study

    International Nuclear Information System (INIS)

    Roy, G.K.; Bhattacharyya, B.

    1997-01-01

    The evolution of the superconducting ground state of the half-filled Penson-Kolb model is examined as a function of the coupling constant using a mean-field approach and the generalized random phase approximation (RPA) in two and three dimensions. On-site singlet pairs hop to compete against single-particle motion in this model, giving the coupling constant a strong momentum dependence. There is a pronounced bandwidth enhancement effect that converges smoothly to a finite value in the strong-coupling (Bose) regime. The low-lying collective excitations evaluated in generalized RPA show a linear dispersion and a gradual crossover from the weak-coupling (BCS) limit to the Bose regime; the mode velocity increases monotonically in sharp contrast to the attractive Hubbard model. Analytical results are derived in the asymptotic limits. copyright 1997 The American Physical Society

  10. Quantum mechanics of the fractional-statistics gas: Random-phase approximation

    International Nuclear Information System (INIS)

    Dai, Q.; Levy, J.L.; Fetter, A.L.; Hanna, C.B.; Laughlin, R.B.

    1992-01-01

    A description of the fractional-statistics gas based on the complete summation of Hartree, Fock, ladder and bubble diagrams is presented. The superfluid properties identified previously in the random-phase-approximation (RPA) calculation of Fetter, Hanna, and Laughlin [Phys. Rev. B 39, 9679 (1989)] are substantially confirmed. The discrepancy between the RPA sound speed and the Hartree-Fock bulk modulus is found to be eliminated. The unusual Hall-effect behavior is found to vanish for the Bose gas test case but not for the fractional-statistics gas, implying that it is physically correct. Excellent agreement is obtained with the collective-mode dispersion obtained numerically by Xie, He, and Das Sarma [Phys. Rev. Lett. 65, 649 (1990)

  11. Dynamic and static correlation functions in the inhomogeneous Hartree-Fock-state approach with random-phase-approximation fluctuations

    International Nuclear Information System (INIS)

    Lorenzana, J.; Grynberg, M.D.; Yu, L.; Yonemitsu, K.; Bishop, A.R.

    1992-11-01

    The ground state energy, and static and dynamic correlation functions are investigated in the inhomogeneous Hartree-Fock (HF) plus random phase approximation (RPA) approach applied to a one-dimensional spinless fermion model showing self-trapped doping states at the mean field level. Results are compared with homogeneous HF and exact diagonalization. RPA fluctuations added to the generally inhomogeneous HF ground state allows the computation of dynamical correlation functions that compare well with exact diagonalization results. The RPA correction to the ground state energy agrees well with the exact results at strong and weak coupling limits. We also compare it with a related quasi-boson approach. The instability towards self-trapped behaviour is signaled by a RPA mode with frequency approaching zero. (author). 21 refs, 10 figs

  12. Hubbard-U corrected Hamiltonians for non-self-consistent random-phase approximation total-energy calculations

    DEFF Research Database (Denmark)

    Patrick, Christopher; Thygesen, Kristian Sommer

    2016-01-01

    In non-self-consistent calculations of the total energy within the random-phase approximation (RPA) for electronic correlation, it is necessary to choose a single-particle Hamiltonian whose solutions are used to construct the electronic density and noninteracting response function. Here we...... investigate the effect of including a Hubbard-U term in this single-particle Hamiltonian, to better describe the on-site correlation of 3d electrons in the transitionmetal compounds ZnS, TiO2, and NiO.We find that the RPA lattice constants are essentially independent of U, despite large changes...... in the underlying electronic structure. We further demonstrate that the non-selfconsistent RPA total energies of these materials have minima at nonzero U. Our RPA calculations find the rutile phase of TiO2 to be more stable than anatase independent of U, a result which is consistent with experiments...

  13. Atomic structure calculations using the relativistic random phase approximation

    International Nuclear Information System (INIS)

    Cheng, K.T.; Johnson, W.R.

    1981-01-01

    A brief review is given for the relativistic random phase approximation (RRPA) applied to atomic transition problems. Selected examples of RRPA calculations on discrete excitations and photoionization are given to illustrate the need of relativistic many-body theories in dealing with atomic processes where both relativity and correlation are important

  14. Accurate and Efficient Parallel Implementation of an Effective Linear-Scaling Direct Random Phase Approximation Method.

    Science.gov (United States)

    Graf, Daniel; Beuerle, Matthias; Schurkus, Henry F; Luenser, Arne; Savasci, Gökcen; Ochsenfeld, Christian

    2018-05-08

    An efficient algorithm for calculating the random phase approximation (RPA) correlation energy is presented that is as accurate as the canonical molecular orbital resolution-of-the-identity RPA (RI-RPA) with the important advantage of an effective linear-scaling behavior (instead of quartic) for large systems due to a formulation in the local atomic orbital space. The high accuracy is achieved by utilizing optimized minimax integration schemes and the local Coulomb metric attenuated by the complementary error function for the RI approximation. The memory bottleneck of former atomic orbital (AO)-RI-RPA implementations ( Schurkus, H. F.; Ochsenfeld, C. J. Chem. Phys. 2016 , 144 , 031101 and Luenser, A.; Schurkus, H. F.; Ochsenfeld, C. J. Chem. Theory Comput. 2017 , 13 , 1647 - 1655 ) is addressed by precontraction of the large 3-center integral matrix with the Cholesky factors of the ground state density reducing the memory requirements of that matrix by a factor of [Formula: see text]. Furthermore, we present a parallel implementation of our method, which not only leads to faster RPA correlation energy calculations but also to a scalable decrease in memory requirements, opening the door for investigations of large molecules even on small- to medium-sized computing clusters. Although it is known that AO methods are highly efficient for extended systems, where sparsity allows for reaching the linear-scaling regime, we show that our work also extends the applicability when considering highly delocalized systems for which no linear scaling can be achieved. As an example, the interlayer distance of two covalent organic framework pore fragments (comprising 384 atoms in total) is analyzed.

  15. Low-lying dipole response in the stable 40,48Ca nuclei within the second random-phase approximation

    International Nuclear Information System (INIS)

    Gambacurta, D.; Grasso, M.; Catara, F.

    2012-01-01

    The low-lying dipole strength distributions of 40 CaCa and 48 Ca, in the energy region between 5 and 10 MeV, are studied within the second random phase approximation (RPA) with Skyrme interaction. Standard RPA models do not usually predict any presence of strength in this energy region, while experimentally a significant amount of strength is found. The inclusion of the 2 particle −2 hole configurations allows to obtain a description in a rather good agreement with the experimental data. The properties of the most collective state are analyzed in terms of its 1 particle −1 hole nature and its transition densities.

  16. Low-lying dipole response in the stable 40,48Ca nuclei within the second random-phase approximation

    Science.gov (United States)

    Gambacurta, D.; Grasso, M.; Catara, F.

    2012-10-01

    The low-lying dipole strength distributions of 40CaCa and 48Ca, in the energy region between 5 and 10 MeV, are studied within the second random phase approximation (RPA) with Skyrme interaction. Standard RPA models do not usually predict any presence of strength in this energy region, while experimentally a significant amount of strength is found. The inclusion of the 2 particle -2 hole configurations allows to obtain a description in a rather good agreement with the experimental data. The properties of the most collective state are analyzed in terms of its 1 particle -1 hole nature and its transition densities.

  17. Density functional formulation of the random-phase approximation for inhomogeneous fluids: Application to the Gaussian core and Coulomb particles.

    Science.gov (United States)

    Frydel, Derek; Ma, Manman

    2016-06-01

    Using the adiabatic connection, we formulate the free energy in terms of the correlation function of a fictitious system, h_{λ}(r,r^{'}), in which interactions λu(r,r^{'}) are gradually switched on as λ changes from 0 to 1. The function h_{λ}(r,r^{'}) is then obtained from the inhomogeneous Ornstein-Zernike equation and the two equations constitute a general liquid-state framework for treating inhomogeneous fluids. The two equations do not yet constitute a closed set. In the present work we use the closure c_{λ}(r,r^{'})≈-λβu(r,r^{'}), known as the random-phase approximation (RPA). We demonstrate that the RPA is identical with the variational Gaussian approximation derived within the field-theoretical framework, originally derived and used for charged particles. We apply our generalized RPA approximation to the Gaussian core model and Coulomb charges.

  18. Linear-scaling implementation of the direct random-phase approximation

    International Nuclear Information System (INIS)

    Kállay, Mihály

    2015-01-01

    We report the linear-scaling implementation of the direct random-phase approximation (dRPA) for closed-shell molecular systems. As a bonus, linear-scaling algorithms are also presented for the second-order screened exchange extension of dRPA as well as for the second-order Møller–Plesset (MP2) method and its spin-scaled variants. Our approach is based on an incremental scheme which is an extension of our previous local correlation method [Rolik et al., J. Chem. Phys. 139, 094105 (2013)]. The approach extensively uses local natural orbitals to reduce the size of the molecular orbital basis of local correlation domains. In addition, we also demonstrate that using natural auxiliary functions [M. Kállay, J. Chem. Phys. 141, 244113 (2014)], the size of the auxiliary basis of the domains and thus that of the three-center Coulomb integral lists can be reduced by an order of magnitude, which results in significant savings in computation time. The new approach is validated by extensive test calculations for energies and energy differences. Our benchmark calculations also demonstrate that the new method enables dRPA calculations for molecules with more than 1000 atoms and 10 000 basis functions on a single processor

  19. Rocksalt or cesium chloride: Investigating the relative stability of the cesium halide structures with random phase approximation based methods

    Science.gov (United States)

    Nepal, Niraj K.; Ruzsinszky, Adrienn; Bates, Jefferson E.

    2018-03-01

    The ground state structural and energetic properties for rocksalt and cesium chloride phases of the cesium halides were explored using the random phase approximation (RPA) and beyond-RPA methods to benchmark the nonempirical SCAN meta-GGA and its empirical dispersion corrections. The importance of nonadditivity and higher-order multipole moments of dispersion in these systems is discussed. RPA generally predicts the equilibrium volume for these halides within 2.4% of the experimental value, while beyond-RPA methods utilizing the renormalized adiabatic LDA (rALDA) exchange-correlation kernel are typically within 1.8%. The zero-point vibrational energy is small and shows that the stability of these halides is purely due to electronic correlation effects. The rAPBE kernel as a correction to RPA overestimates the equilibrium volume and could not predict the correct phase ordering in the case of cesium chloride, while the rALDA kernel consistently predicted results in agreement with the experiment for all of the halides. However, due to its reasonable accuracy with lower computational cost, SCAN+rVV10 proved to be a good alternative to the RPA-like methods for describing the properties of these ionic solids.

  20. Assessing the performance of the random phase approximation for exchange and superexchange coupling constants in magnetic crystalline solids

    DEFF Research Database (Denmark)

    Olsen, Thomas

    2017-01-01

    The random phase approximation (RPA) for total energies has previously been shown to provide a qualitatively correct description of static correlation in molecular systems, where density functional theory (DFT) with local functionals are bound to fail. This immediately poses the question of whether...... the RPA is also able to capture the correct physics of strongly correlated solids such asMott insulators. Due to strong electron localization, magnetic interactions in such systems are dominated by superexchange, which in the simplest picture can be regarded as the analog of static correlation...... for molecules. In this paper, we investigate the performance of the RPA for evaluating both superexchange and direct exchange interactions in the magnetic solids NiO, MnO, Na3Cu2SbO6, Sr2CuO3, Sr2CuTeO6, and a monolayer of CrI3, which were chosen to represent a broad variety of magnetic interactions...

  1. Relativistic quasiparticle random phase approximation in deformed nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Pena Arteaga, D.

    2007-06-25

    Covariant density functional theory is used to study the influence of electromagnetic radiation on deformed superfluid nuclei. The relativistic Hartree-Bogolyubov equations and the resulting diagonalization problem of the quasiparticle random phase approximation are solved for axially symmetric systems in a fully self-consistent way by a newly developed parallel code. Three different kinds of high precision energy functionals are investigated and special care is taken for the decoupling of the Goldstone modes. This allows the microscopic investigation of Pygmy and scissor resonances in electric and magnetic dipole fields. Excellent agreement with recent experiments is found and new types of modes are predicted for deformed systems with large neutron excess. (orig.)

  2. Photons in dense nuclear matter: Random-phase approximation

    Science.gov (United States)

    Stetina, Stephan; Rrapaj, Ermal; Reddy, Sanjay

    2018-04-01

    We present a comprehensive and pedagogic discussion of the properties of photons in cold and dense nuclear matter based on the resummed one-loop photon self-energy. Correlations among electrons, muons, protons, and neutrons in β equilibrium that arise as a result of electromagnetic and strong interactions are consistently taken into account within the random phase approximation. Screening effects, damping, and collective excitations are systematically studied in a fully relativistic setup. Our study is relevant to the linear response theory of dense nuclear matter, calculations of transport properties of cold dense matter, and investigations of the production and propagation of hypothetical vector bosons such as the dark photons.

  3. Fast computation of molecular random phase approximation correlation energies using resolution of the identity and imaginary frequency integration

    Science.gov (United States)

    Eshuis, Henk; Yarkony, Julian; Furche, Filipp

    2010-06-01

    The random phase approximation (RPA) is an increasingly popular post-Kohn-Sham correlation method, but its high computational cost has limited molecular applications to systems with few atoms. Here we present an efficient implementation of RPA correlation energies based on a combination of resolution of the identity (RI) and imaginary frequency integration techniques. We show that the RI approximation to four-index electron repulsion integrals leads to a variational upper bound to the exact RPA correlation energy if the Coulomb metric is used. Auxiliary basis sets optimized for second-order Møller-Plesset (MP2) calculations are well suitable for RPA, as is demonstrated for the HEAT [A. Tajti et al., J. Chem. Phys. 121, 11599 (2004)] and MOLEKEL [F. Weigend et al., Chem. Phys. Lett. 294, 143 (1998)] benchmark sets. Using imaginary frequency integration rather than diagonalization to compute the matrix square root necessary for RPA, evaluation of the RPA correlation energy requires O(N4 log N) operations and O(N3) storage only; the price for this dramatic improvement over existing algorithms is a numerical quadrature. We propose a numerical integration scheme that is exact in the two-orbital case and converges exponentially with the number of grid points. For most systems, 30-40 grid points yield μH accuracy in triple zeta basis sets, but much larger grids are necessary for small gap systems. The lowest-order approximation to the present method is a post-Kohn-Sham frequency-domain version of opposite-spin Laplace-transform RI-MP2 [J. Jung et al., Phys. Rev. B 70, 205107 (2004)]. Timings for polyacenes with up to 30 atoms show speed-ups of two orders of magnitude over previous implementations. The present approach makes it possible to routinely compute RPA correlation energies of systems well beyond 100 atoms, as is demonstrated for the octapeptide angiotensin II.

  4. Isoscalar compression modes in relativistic random phase approximation

    International Nuclear Information System (INIS)

    Ma, Zhong-yu; Van Giai, Nguyen.; Wandelt, A.; Vretenar, D.; Ring, P.

    2001-01-01

    Monopole and dipole compression modes in nuclei are analyzed in the framework of a fully consistent relativistic random phase approximation (RRPA), based on effective mean-field Lagrangians with nonlinear meson self-interaction terms. The large effect of Dirac sea states on isoscalar strength distribution functions is illustrated for the monopole mode. The main contribution of Fermi and Dirac sea pair states arises through the exchange of the scalar meson. The effect of vector meson exchange is much smaller. For the monopole mode, RRPA results are compared with constrained relativistic mean-field calculations. A comparison between experimental and calculated energies of isoscalar giant monopole resonances points to a value of 250-270 MeV for the nuclear matter incompressibility. A large discrepancy remains between theoretical predictions and experimental data for the dipole compression mode

  5. Relativistic quasiparticle random phase approximation with a separable pairing force

    International Nuclear Information System (INIS)

    Tian Yuan; Ma Zhongyu; Ring Peter

    2009-01-01

    In our previous work, we introduced a separable pairing force for relativistic Hartree-Bogoliubov calculations. This force was adjusted to reproduce the pairing properties of the Gogny force in nuclear matter. By using the well known techniques of Talmi and Moshinsky it can be expanded in a series of separable terms and converges quickly after a few terms. It was found that the pairing properties can be depicted on almost the same footing as the original pairing interaction, not only in nuclear matter, but also in finite nuclei. In this study, we construct a relativistic quasiparticle random phase approximation (RQRPA) with this separable pairing interaction and calculate the excitation energies of the first excited 2 + states and reduced B(E2; 0 + →2 + ) transition rates for a chain of Sn isotopes in RQRPA. Compared with the results of the full Gogny force, we find that this simple separable pairing interaction can describe the pairing properties of the excited vibrational states as well as the original pairing interaction. (authors)

  6. Separable pairing force for relativistic quasiparticle random-phase approximation

    International Nuclear Information System (INIS)

    Tian Yuan; Ma Zhongyu; Ring, Peter

    2009-01-01

    We have introduced a separable pairing force, which was adjusted to reproduce the pairing properties of the Gogny force in nuclear matter. This separable pairing force is able to describe in relativistic Hartree-Bogoliubov (RHB) calculations the pairing properties in the ground state of finite nuclei on almost the same footing as the original Gogny interaction. In this work we investigate excited states using the Relativistic Quasiparticle Random-Phase Approximation (RQRPA) with the same separable pairing force. For consistency the Goldstone modes and the convergence with various cutoff parameters in this version of RQRPA are studied. The first excited 2 + states for the chain of Sn isotopes with Z=50 and the chain of isotones with N=82 isotones are calculated in RQRPA together with the 3 - states of Sn isotopes. By comparing our results with experimental data and with the results of the original Gogny force we find that this simple separable pairing interaction is very successful in depicting the pairing properties of vibrational excitations.

  7. Vanishing-Overhead Linear-Scaling Random Phase Approximation by Cholesky Decomposition and an Attenuated Coulomb-Metric.

    Science.gov (United States)

    Luenser, Arne; Schurkus, Henry F; Ochsenfeld, Christian

    2017-04-11

    A reformulation of the random phase approximation within the resolution-of-the-identity (RI) scheme is presented, that is competitive to canonical molecular orbital RI-RPA already for small- to medium-sized molecules. For electronically sparse systems drastic speedups due to the reduced scaling behavior compared to the molecular orbital formulation are demonstrated. Our reformulation is based on two ideas, which are independently useful: First, a Cholesky decomposition of density matrices that reduces the scaling with basis set size for a fixed-size molecule by one order, leading to massive performance improvements. Second, replacement of the overlap RI metric used in the original AO-RPA by an attenuated Coulomb metric. Accuracy is significantly improved compared to the overlap metric, while locality and sparsity of the integrals are retained, as is the effective linear scaling behavior.

  8. High-K precession modes: Axially symmetric limit of wobbling motion in the cranked random-phase approximation description

    International Nuclear Information System (INIS)

    Shimizu, Yoshifumi R.; Matsuzaki, Masayuki; Matsuyanagi, Kenichi

    2005-01-01

    The rotational band built on the high-K multi-quasiparticle state can be interpreted as a multi-phonon band of the precession mode, which represents the precessional rotation about the axis perpendicular to the direction of the intrinsic angular momentum. By using the axially symmetric limit of the random-phase approximation (RPA) formalism developed for the nuclear wobbling motion, we study the properties of the precession modes in 178 W: the excitation energies, B(E2) and B(M1) values. We show that the excitations of such a specific type of rotation can be well described by the RPA formalism, which gives new insight into the wobbling motion in the triaxial superdeformed nuclei from a microscopic viewpoint

  9. Surface wake in the random-phase approximation

    International Nuclear Information System (INIS)

    Garcia de Abajo, F.J.; Echenique, P.M.

    1993-01-01

    The scalar-electric-potential distribution set up by an ion traveling in the vicinity of a plane solid-vacuum interface, that is, the surface-wake potential, is investigated with the specular-reflection model to describe the response of the surface and with the random-phase approximation for the dielectric function of the bulk material. This permits us to address the study of the low-velocity surface wake: the static potential is found to have a dip at the position of the ion; that dip is shifted towards the direction opposite to the velocity vector for velocities smaller than the threshold of creation of plasmons (∼1.3v F ). Extensive numerical calculations are presented for an ion both inside and outside aluminum. Comparison to the results obtained with the plasmon-pole dielectric function indicates excellent agreement for velocities larger than ∼1.3v F . On the other side, the possibility of surface-wake riding is suggested, by analogy with bulk-wake riding postulated in the past. In it, the electron would be bound in the first trough of the surface-wake potential set up when the ion describes a grazing trajectory. The main feature introduced by the surface with respect to the bulk consists of allowing the use of ions of higher charge, reducing in this way the relative importance of the electron self-energy, and in addition, giving rise to larger binding energies. When the ion beam is directed along a special direction of an oriented crystal surface, the mechanism of resonant coherent excitation could provide a way for experimentally detecting this phenomenon through the emission of the bound electron with well-defined energy and around a preferential direction

  10. The time-dependent relativistic mean-field theory and the random phase approximation

    International Nuclear Information System (INIS)

    Ring, P.; Ma, Zhong-yu; Van Giai, Nguyen; Vretenar, D.; Wandelt, A.; Cao, Li-gang

    2001-01-01

    The Relativistic Random Phase Approximation (RRPA) is derived from the Time-Dependent Relativistic Mean-Field (TD RMF) theory in the limit of small amplitude oscillations. In the no-sea approximation of the RMF theory, the RRPA configuration space includes not only the usual particle-hole ph-states, but also αh-configurations, i.e. pairs formed from occupied states in the Fermi sea and empty negative-energy states in the Dirac sea. The contribution of the negative-energy states to the RRPA matrices is examined in a schematic model, and the large effect of Dirac-sea states on isoscalar strength distributions is illustrated for the giant monopole resonance in 116 Sn. It is shown that, because the matrix elements of the time-like component of the vector-meson fields which couple the αh-configurations with the ph-configurations are strongly reduced with respect to the corresponding matrix elements of the isoscalar scalar meson field, the inclusion of states with unperturbed energies more than 1.2 GeV below the Fermi energy has a pronounced effect on giant resonances with excitation energies in the MeV region. The influence of nuclear magnetism, i.e. the effect of the spatial components of the vector fields is examined, and the difference between the nonrelativistic and relativistic RPA predictions for the nuclear matter compression modulus is explained

  11. Communication: An effective linear-scaling atomic-orbital reformulation of the random-phase approximation using a contracted double-Laplace transformation

    International Nuclear Information System (INIS)

    Schurkus, Henry F.; Ochsenfeld, Christian

    2016-01-01

    An atomic-orbital (AO) reformulation of the random-phase approximation (RPA) correlation energy is presented allowing to reduce the steep computational scaling to linear, so that large systems can be studied on simple desktop computers with fully numerically controlled accuracy. Our AO-RPA formulation introduces a contracted double-Laplace transform and employs the overlap-metric resolution-of-the-identity. First timings of our pilot code illustrate the reduced scaling with systems comprising up to 1262 atoms and 10 090 basis functions. 

  12. Low-lying dipole response in the stable {sup 40,48}Ca nuclei within the second random-phase approximation

    Energy Technology Data Exchange (ETDEWEB)

    Gambacurta, D.; Grasso, M.; Catara, F. [GANIL,CEA/DSM-CNRS/IN2P3, Caen (France); Institut de Physique Nucleaire, Universite Paris-Sud, IN2P3-CNRS, F-91406 Orsay Cedex (France); Dipartimento di Fisica e Astronomia dell' Universita di and INFN Catania (Italy)

    2012-10-20

    The low-lying dipole strength distributions of {sup 40}CaCa and {sup 48}Ca, in the energy region between 5 and 10 MeV, are studied within the second random phase approximation (RPA) with Skyrme interaction. Standard RPA models do not usually predict any presence of strength in this energy region, while experimentally a significant amount of strength is found. The inclusion of the 2 particle -2 hole configurations allows to obtain a description in a rather good agreement with the experimental data. The properties of the most collective state are analyzed in terms of its 1 particle -1 hole nature and its transition densities.

  13. Self-consistent random phase approximation - application to systems of strongly correlated fermions

    International Nuclear Information System (INIS)

    Jemai, M.

    2004-07-01

    In the present thesis we have applied the self consistent random phase approximation (SCRPA) to the Hubbard model with a small number of sites (a chain of 2, 4, 6,... sites). Earlier SCRPA had produced very good results in other models like the pairing model of Richardson. It was therefore interesting to see what kind of results the method is able to produce in the case of a more complex model like the Hubbard model. To our great satisfaction the case of two sites with two electrons (half-filling) is solved exactly by the SCRPA. This may seem a little trivial but the fact is that other respectable approximations like 'GW' or the approach with the Gutzwiller wave function yield results still far from exact. With this promising starting point, the case of 6 sites at half filling was considered next. For that case, evidently, SCRPA does not any longer give exact results. However, they are still excellent for a wide range of values of the coupling constant U, covering for instance the phase transition region towards a state with non zero magnetisation. We consider this as a good success of the theory. Non the less the case of 4 sites (a plaquette), as indeed all cases with 4n sites at half filling, turned out to have a problem because of degeneracies at the Hartree Fock level. A generalisation of the present method, including in addition to the pairs, quadruples of Fermions operators (called second RPA) is proposed to also include exactly the plaquette case in our approach. This is therefore a very interesting perspective of the present work. (author)

  14. Second RPA with Skyrme Interaction

    International Nuclear Information System (INIS)

    Gambacurta, D; Catara, F; Grasso, M

    2011-01-01

    The Second Random Phase Approximation (RPA) is a natural extension of RPA obtained by introducing more general excitation operators where two particle-two hole configurations, in addition to the one particle-one hole ones, are considered. Some Second RPA results with Skyrme force in 16 O are presented. Different levels of approximation are compared and in particular the quality of the diagonal approximation is tested. The issue of the rearrangement terms to be used in the matrix elements beyond the standard RPA ones, when density-dependent force are used, is briefly discussed. Two approximated, and generally used, schemes are used: the rearrangement terms are neglected in the matrix elements beyond RPA or evaluated with the RPA prescription. As a general feature of Second RPA results, a several-MeV shift of the strength distribution to lower energies is systematically found with respect to RPA distributions.

  15. Number-conserving random phase approximation with analytically integrated matrix elements

    International Nuclear Information System (INIS)

    Kyotoku, M.; Schmid, K.W.; Gruemmer, F.; Faessler, A.

    1990-01-01

    In the present paper a number conserving random phase approximation is derived as a special case of the recently developed random phase approximation in general symmetry projected quasiparticle mean fields. All the occurring integrals induced by the number projection are performed analytically after writing the various overlap and energy matrices in the random phase approximation equation as polynomials in the gauge angle. In the limit of a large number of particles the well-known pairing vibration matrix elements are recovered. We also present a new analytically number projected variational equation for the number conserving pairing problem

  16. Photoabsorption for helium, lithium, and beryllium atoms in the random-phase approximation with exchange

    International Nuclear Information System (INIS)

    Amusia, M.Y.; Cherepkov, N.A.; Zivanovic, D.; Radojevic, V.

    1976-01-01

    The photoionization cross sections and the oscillator strengths for helium, lithium, and beryllium atoms are calculated in the framework of the random-phase approximation with exchange. The energy-level shift for discrete transitions is taken into account consistently in this approximation. The results are compared with other many-body calculations and with experimental data. The comparison shows that the random-phase approximation with exchange can even be used for systems with a small number of particles

  17. Optimized random phase approximation for the structure of liquid alkali metals as electron-ion plasmas

    International Nuclear Information System (INIS)

    Senatore, G.; Tosi, M.P.; Trieste Univ.

    1981-08-01

    The purpose of this letter is to stress that the way towards an unconventional optimized-random-phase-approximation (ORPA) approach to the structure of liquid metals is indicated, and in fact already a good first-order solution for such an approach is provided

  18. First-order corrections to random-phase approximation GW calculations in silicon and diamond

    NARCIS (Netherlands)

    Ummels, R.T.M.; Bobbert, P.A.; van Haeringen, W.

    1998-01-01

    We report on ab initio calculations of the first-order corrections in the screened interaction W to the random-phase approximation polarizability and to the GW self-energy, using a noninteracting Green's function, for silicon and diamond. It is found that the first-order vertex and self-consistency

  19. Self-consistent Random Phase Approximation applied to a schematic model of the field theory; Approximation des phases aleatoires self-consistante appliquee a un modele schematique de la theorie des champs

    Energy Technology Data Exchange (ETDEWEB)

    Bertrand, Thierry [Inst. de Physique Nucleaire, Lyon-1 Univ., 69 - Villeurbanne (France)

    1998-12-11

    The self-consistent Random Phase Approximation (SCRPA) is a method allowing in the mean-field theory inclusion of the correlations in the ground and excited states. It has the advantage of not violating the Pauli principle in contrast to RPA, that is based on the quasi-bosonic approximation; in addition, numerous applications in different domains of physics, show a possible variational character. However, the latter should be formally demonstrated. The first model studied with SCRPA is the anharmonic oscillator in the region where one of its symmetries is spontaneously broken. The ground state energy is reproduced by SCRPA more accurately than RPA, with no violation of the Ritz variational principle, what is not the case for the latter approximation. The success of SCRPA is the the same in case of ground state energy for a model mixing bosons and fermions. At the transition point the SCRPA is correcting RPA drastically, but far from this region the correction becomes negligible, both methods being of similar precision. In the deformed region in the case of RPA a spurious mode occurred due to the microscopical character of the model.. The SCRPA may also reproduce this mode very accurately and actually it coincides with an excitation in the exact spectrum 40 refs., 33 figs., 14 tabs.

  20. Calculating beta decay in the deformed self-consistent quasiparticle random phase approximation

    Energy Technology Data Exchange (ETDEWEB)

    Engel, Jonathan, E-mail: engelj@physics.unc.edu [Department of Physics and Astronomy, University of North Carolina, Chapel Hill, NC 27599-3255 (United States); Mustonen, M. T., E-mail: mika.mustonen@yale.edu [Department of Physics and Astronomy, University of North Carolina, Chapel Hill, NC 27599-3255 (United States); Center for Theoretical Physics, Sloane Physics Laboratory, Yale University, New Haven, CT 06052 (United States)

    2016-06-21

    We discuss a recent global calculation of beta-decay rates in the self-consistent Skyrme quasiparticle random phase approximation (QRPA), with axially symmetric nuclear deformation treated explicitly. The calculation makes makes use of the finite-amplitude method, first proposed by Nakatsukasa and collaborators, to reduce computation time. The results are comparable in quality to those of several other global QRPA calculations. The QRPA may have reached the limit of its accuracy.

  1. Neutrino-nucleus reaction rates based on the relativistic quasiparticle random phase approximation

    International Nuclear Information System (INIS)

    Paar, N.; Vretenar, D.; Marketin, T.; Ring, P.

    2008-01-01

    Neutrino-nucleus cross sections are described in a novel theoretical framework where the weak interaction of leptons with hadrons is expressed in the standard current-current form, the nuclear ground state is described in the relativistic Hartree-Bogoliubov model, and the relevant transitions to excited states are calculated in the relativistic quasiparticle random phase approximation. The model is employed in studies of neutrino-nucleus reactions in several test cases

  2. The RPA Atomization Energy Puzzle.

    Science.gov (United States)

    Ruzsinszky, Adrienn; Perdew, John P; Csonka, Gábor I

    2010-01-12

    There is current interest in the random phase approximation (RPA), a "fifth-rung" density functional for the exchange-correlation energy. RPA has full exact exchange and constructs the correlation with the help of the unoccupied Kohn-Sham orbitals. In many cases (uniform electron gas, jellium surface, and free atom), the correction to RPA is a short-ranged effect that is captured by a local spin density approximation (LSDA) or a generalized gradient approximation (GGA). Nonempirical density functionals for the correction to RPA were constructed earlier at the LSDA and GGA levels (RPA+), but they are constructed here at the fully nonlocal level (RPA++), using the van der Waals density functional (vdW-DF) of Langreth, Lundqvist, and collaborators. While they make important and helpful corrections to RPA total and ionization energies of free atoms, they correct the RPA atomization energies of molecules by only about 1 kcal/mol. Thus, it is puzzling that RPA atomization energies are, on average, about 10 kcal/mol lower than those of accurate values from experiment. We find here that a hybrid of 50% Perdew-Burke-Ernzerhof GGA with 50% RPA+ yields atomization energies much more accurate than either one does alone. This suggests a solution to the puzzle: While the proper correction to RPA is short-ranged in some systems, its contribution to the correlation hole can spread out in a molecule with multiple atomic centers, canceling part of the spread of the exact exchange hole (more so than in RPA or RPA+), making the true exchange-correlation hole more localized than in RPA or RPA+. This effect is not captured even by the vdW-DF nonlocality, but it requires the different kind of full nonlocality present in a hybrid functional.

  3. Finite-temperature random-phase approximation for spectroscopic properties of neon plasmas

    International Nuclear Information System (INIS)

    Colgan, J.; Collins, L. A.; Fontes, C. J.; Csanak, G.

    2007-01-01

    A finite-temperature random-phase approximation (FTRPA) is applied to calculate oscillator strengths for excitations in hot and dense plasmas. Application of the FTRPA provides a convenient, self-consistent method with which to explore coupled-channel effects of excited electrons in a dense plasma. We present FTRPA calculations that include coupled-channel effects. The inclusion of these effects is shown to cause significant differences in the oscillator strength for a prototypical case of 1 P excitation in neon when compared with single-channel and with average-atom calculations. Trends as a function of temperature and density are also discussed

  4. Effects of thermal and particle-number fluctuations on the giant isovector dipole modes for the 58Ni nucleus in the finite-temperature random-phase approximation

    International Nuclear Information System (INIS)

    Nguyen Dinhdang; Nguyen Zuythang

    1988-01-01

    Using the realistic single-particle energy spectrum obtained in the Woods-Saxon nucleon mean-field potential, we calculate the BCS pairing gap for 58 Ni as a function of temperature taking into account the thermal and particle-number fluctuations. The strength distributions of the electric dipole transitions and the centroids of the isovector giant dipole resonance (IV-GDR) are computed in the framework of the finite-temperature random-phase approximation (RPA) based on the Hamiltonian of the quasiparticle-phonon nuclear model with separate dipole forces. It is shown that the change of the pairing gap at finite temperature can noticeably influence the IV-GDR localisation in realistic nuclei. By taking both thermal and quasiparticle fluctuations in the pairing gap into account the effect of the phase transition from superfluid to normal in the temperature dependence of the IV-GDR centroid is completely smeared out. (author)

  5. Importance of self-consistency in relativistic continuum random-phase approximation calculations

    International Nuclear Information System (INIS)

    Yang Ding; Cao Ligang; Tian Yuan; Ma Zhongyu

    2010-01-01

    A fully consistent relativistic continuum random phase approximation (RCRPA) is constructed, where the contribution of the continuum spectrum to nuclear excitations is treated exactly by the single-particle Green's function technique. The full consistency of the calculations is achieved that the same effective Lagrangian is adopted for the ground state and the excited states. The negative energy states in the Dirac sea are also included in the single-particle Green's function in the no-sea approximation. The currents from the vector meson and photon exchanges and the Coulomb interaction in RCRPA are treated exactly. The spin-orbit interaction is included naturally in the relativistic frame. Numerical results of the RCRPA are checked with the constrained relativistic mean-field theory. We study the effects of the inconsistency, particularly the currents and Coulomb interaction in various collective multipole excitations.

  6. Extended random-phase approximation with three-body ground-state correlations

    International Nuclear Information System (INIS)

    Tohyama, M.; Schuck, P.

    2008-01-01

    An extended random-phase approximation (ERPA) which contains the effects of ground-state correlations up to a three-body level is applied to an extended Lipkin model which contains an additional particle-scattering term. Three-body correlations in the ground state are necessary to preserve the hermiticity of the Hamiltonian matrix of ERPA. Two approximate forms of ERPA which neglect the three-body correlations are also applied to investigate the importance of three-body correlations. It is found that the ground-state energy is little affected by the inclusion of the three-body correlations. On the contrary, three-body correlations for the excited states can become quite important. (orig.)

  7. Self-consistent random phase approximation - application to systems of strongly correlated fermions; Approximation des phases aleatoires self-consistante - applications a des systemes de fermions fortement correles

    Energy Technology Data Exchange (ETDEWEB)

    Jemai, M

    2004-07-01

    In the present thesis we have applied the self consistent random phase approximation (SCRPA) to the Hubbard model with a small number of sites (a chain of 2, 4, 6,... sites). Earlier SCRPA had produced very good results in other models like the pairing model of Richardson. It was therefore interesting to see what kind of results the method is able to produce in the case of a more complex model like the Hubbard model. To our great satisfaction the case of two sites with two electrons (half-filling) is solved exactly by the SCRPA. This may seem a little trivial but the fact is that other respectable approximations like 'GW' or the approach with the Gutzwiller wave function yield results still far from exact. With this promising starting point, the case of 6 sites at half filling was considered next. For that case, evidently, SCRPA does not any longer give exact results. However, they are still excellent for a wide range of values of the coupling constant U, covering for instance the phase transition region towards a state with non zero magnetisation. We consider this as a good success of the theory. Non the less the case of 4 sites (a plaquette), as indeed all cases with 4n sites at half filling, turned out to have a problem because of degeneracies at the Hartree Fock level. A generalisation of the present method, including in addition to the pairs, quadruples of Fermions operators (called second RPA) is proposed to also include exactly the plaquette case in our approach. This is therefore a very interesting perspective of the present work. (author)

  8. Random phase approximations for the screening function in high Tc superconductors

    International Nuclear Information System (INIS)

    Lopez-Aguilar, F.; Costa-Quintana, J.; Sanchez, A.; Puig, T.; Aurell, M.T.; Martinez, L.M.; Munoz, J.S.

    1990-01-01

    This paper reports on the electronic transferences from the CuO 2 sheets toward the CuO 3 linear chain, which locate electrons in the orbitals p y /p z of O4/O1 and d z 2 -y 2 of Cu1, and holes in the orbitals d x 2 -y 2 - P z /p y of Cu2 - P2/O3. These holes states present large interatomic overlapping. In this paper, we determine the screening function within the random phase approximation applied to the high-T c superconductors. This screening function is vanishing for determined values of the frequency which correspond to renormalized plasmon frequencies. These frequencies depends on the band parameters and their knowledge is essential for determining the self energy. This self energy is deduced and it contain independent terms for each of the channels for the localization

  9. Finite nucleus Dirac mean field theory and random phase approximation using finite B splines

    International Nuclear Information System (INIS)

    McNeil, J.A.; Furnstahl, R.J.; Rost, E.; Shepard, J.R.; Department of Physics, University of Maryland, College Park, Maryland 20742; Department of Physics, University of Colorado, Boulder, Colorado 80309)

    1989-01-01

    We calculate the finite nucleus Dirac mean field spectrum in a Galerkin approach using finite basis splines. We review the method and present results for the relativistic σ-ω model for the closed-shell nuclei 16 O and 40 Ca. We study the convergence of the method as a function of the size of the basis and the closure properties of the spectrum using an energy-weighted dipole sum rule. We apply the method to the Dirac random-phase-approximation response and present results for the isoscalar 1/sup -/ and 3/sup -/ longitudinal form factors of 16 O and 40 Ca. We also use a B-spline spectral representation of the positive-energy projector to evaluate partial energy-weighted sum rules and compare with nonrelativistic sum rule results

  10. Thermodynamics and structure of liquid metals from a consistent optimized random phase approximation

    International Nuclear Information System (INIS)

    Akinlade, O.; Badirkhan, Z.; Pastore, G.

    2000-05-01

    We study thermodynamics and structural properties of several liquid metals to assess the validity of the generalized non-local model potential (GNMP) of Li et. al. [J.Phys. F16,309 (1986)]. By using a new thermodynamically consistent version of the optimized random phase approximation (ORPA), especially adapted to continuous reference potentials, we improve our previous results obtained within the variational approach based on the Gibbs - Bogoliubov inequality. Hinging on the unified and very accurate evaluation of structure factors and thermodynamic quantities provided by the ORPA, we find that the GNMP yields satisfactory results for the alkali metals, however, those for the polyvalent metals point to a substantial inadequacy of the GNMP for high valence systems. (author)

  11. Relativistic Random-Phase Approximation with Density-dependent Meson-nucleon Couplings at Finite Temperature

    International Nuclear Information System (INIS)

    Niu, Y.; Paar, N.; Vretenar, D.; Meng, J.

    2009-01-01

    The fully self-consistent relativistic random-phase approximation (RRPA) framework based on effective interactions with a phenomenological density dependence is extended to finite temperatures. The RRPA configuration space is built from the spectrum of single-nucleon states at finite temperature obtained by the temperature dependent relativistic mean field (RMF-T) theory based on effective Lagrangian with density dependent meson-nucleon vertex functions. As an illustration, the dependence of binding energy, radius, entropy and single particle levels on temperature for spherical nucleus 2 08P b is investigated in RMF-T theory. The finite temperature RRPA has been employed in studies of giant monopole and dipole resonances, and the evolution of resonance properties has been studied as a function of temperature. In addition, exotic modes of excitation have been systematically explored at finite temperatures, with an emphasis on the case of pygmy dipole resonances.(author)

  12. β-decay rates of r-process nuclei in the relativistic quasiparticle random phase approximation

    International Nuclear Information System (INIS)

    Niksic, T.; Marketin, T.; Vretenar, D.; Paar, N.; Ring, P.

    2004-01-01

    The fully consistent relativistic proton-neutron quasiparticle random phase approximation (PN-RQRPA) is employed in the calculation of β-decay half-lives of neutron-rich nuclei in the N∼50 and N∼82 regions. A new density-dependent effective interaction, with an enhanced value of the nucleon effective mass, is used in relativistic Hartree-Bogolyubov calculation of nuclear ground states and in the particle-hole channel of the PN-RQRPA. The finite range Gogny D1S interaction is employed in the T=1 pairing channel, and the model also includes a proton-neutron particle-particle interaction. The theoretical half-lives reproduce the experimental data for the Fe, Zn, Cd, and Te isotopic chains, but overestimate the lifetimes of Ni isotopes and predict a stable 132 Sn. (orig.)

  13. β-decay rates of r-process nuclei in the relativistic quasiparticle random phase approximation

    International Nuclear Information System (INIS)

    Niksic, T.; Marketin, T.; Vretenar, D.; Paar, N.; Ring, P.

    2005-01-01

    The fully consistent relativistic proton-neutron quasiparticle random phase approximation (PN-RQRPA) is employed in the calculation of β-decay half-lives of neutron-rich nuclei in the N≅50 and N≅82 regions. A new density-dependent effective interaction, with an enhanced value of the nucleon effective mass, is used in relativistic Hartree-Bogoliubov calculation of nuclear ground states and in the particle-hole channel of the PN-RQRPA. The finite range Gogny D1S interaction is employed in the T=1 pairing channel, and the model also includes a proton-neutron particle-particle interaction. The theoretical half-lives reproduce the experimental data for the Fe, Zn, Cd, and Te isotopic chains but overestimate the lifetimes of Ni isotopes and predict a stable 132 Sn

  14. Relativistic quasiparticle random-phase approximation calculation of total muon capture rates

    International Nuclear Information System (INIS)

    Marketin, T.; Paar, N.; Niksic, T.; Vretenar, D.

    2009-01-01

    The relativistic proton-neutron quasiparticle random phase approximation (pn-RQRPA) is applied in the calculation of total muon capture rates on a large set of nuclei from 12 C to 244 Pu, for which experimental values are available. The microscopic theoretical framework is based on the relativistic Hartree-Bogoliubov (RHB) model for the nuclear ground state, and transitions to excited states are calculated using the pn-RQRPA. The calculation is fully consistent, i.e., the same interactions are used both in the RHB equations that determine the quasiparticle basis, and in the matrix equations of the pn-RQRPA. The calculated capture rates are sensitive to the in-medium quenching of the axial-vector coupling constant. By reducing this constant from its free-nucleon value g A =1.262 by 10% for all multipole transitions, the calculation reproduces the experimental muon capture rates to better than 10% accuracy.

  15. {beta}-decay rates of r-process nuclei in the relativistic quasiparticle random phase approximation

    Energy Technology Data Exchange (ETDEWEB)

    Niksic, T.; Marketin, T.; Vretenar, D. [Zagreb Univ. (Croatia). Faculty of Science, Physics Dept.; Paar, N. [Technische Univ. Darmstadt (Germany). Inst. fuer Kernphysik; Ring, P. [Technische Univ. Muenchen, Garching (Germany). Physik-Department

    2004-12-08

    The fully consistent relativistic proton-neutron quasiparticle random phase approximation (PN-RQRPA) is employed in the calculation of {beta}-decay half-lives of neutron-rich nuclei in the N{approx}50 and N{approx}82 regions. A new density-dependent effective interaction, with an enhanced value of the nucleon effective mass, is used in relativistic Hartree-Bogolyubov calculation of nuclear ground states and in the particle-hole channel of the PN-RQRPA. The finite range Gogny D1S interaction is employed in the T=1 pairing channel, and the model also includes a proton-neutron particle-particle interaction. The theoretical half-lives reproduce the experimental data for the Fe, Zn, Cd, and Te isotopic chains, but overestimate the lifetimes of Ni isotopes and predict a stable {sup 132}Sn. (orig.)

  16. The Bogolubov Representation of the Polaron Model and Its Completely Integrable RPA-Approximation

    International Nuclear Information System (INIS)

    Bogolubov, Nikolai N. Jr.; Prykarpatsky, Yarema A.; Ghazaryan, Anna A.

    2009-12-01

    The polaron model in ionic crystal is studied in the N. Bogolubov representation using a special RPA-approximation. A new exactly solvable approximated polaron model is derived and described in detail. Its free energy at finite temperature is calculated analytically. The polaron free energy in the constant magnetic field at finite temperature is also discussed. Based on the structure of the N. Bogolubov unitary transformed polaron Hamiltonian a very important new result is stated: the full polaron model is exactly solvable. (author)

  17. Chiral NNLOsat descriptions of nuclear multipole resonances within the random-phase approximation

    Science.gov (United States)

    Wu, Q.; Hu, B. S.; Xu, F. R.; Ma, Y. Z.; Dai, S. J.; Sun, Z. H.; Jansen, G. R.

    2018-05-01

    We study nuclear multipole resonances in the framework of the random-phase approximation by using the chiral potential NNLOsat. This potential includes two- and three-body terms that have been simultaneously optimized to low-energy nucleon-nucleon scattering data and selected nuclear structure data. Our main focuses have been the isoscalar monopole, isovector dipole, and isoscalar quadrupole resonances of the closed-shell nuclei, 4He, O 16 ,22 ,24 , and Ca,4840. These resonance modes have been widely observed in experiment. In addition, we use a renormalized chiral potential Vlow-k, based on the N3LO two-body potential by Entem and Machleidt [Phys. Rev. C 68, 041001 (2011), 10.1103/PhysRevC.68.041001]. This introduces a dependency on the cutoff parameter used in the normalization procedure as reported in previous works by other groups. While NNLOsat can reasonably reproduce observed multipole resonances, it is not possible to find a single cutoff parameter for the Vlow-k potential that simultaneously describes the different types of resonance modes. The sensitivity to the cutoff parameter can be explained by missing induced three-body forces in the calculations. Our results for neutron-rich O,2422 show a mixing nature of isoscalar and isovector resonances in the dipole channel at low energies. We predict that 22O and 24O have low-energy isoscalar quadrupole resonances at energies lower than 5 MeV.

  18. Studies of Ionic Photoionization Using Relativistic Random Phase Approximation and Relativistic Multichannel Quantum Defect Theory

    Science.gov (United States)

    Haque, Ghousia Nasreen

    The absorption of electromagnetic radiation by positive ions is one of the fundamental processes of nature which occurs in every intensely hot environment. Due to the difficulties in producing sufficient densities of ions in a laboratory, there are very few measurements of ionic photoabsorption parameters. On the theoretical side, some calculations have been made of a few major photoionization parameters, but generally speaking, most of the work done so far has employed rather simple single particle models and any theoretical work which has adequately taken into account intricate atomic many-body and relativistic effects is only scanty. In the present work, several complex aspects of atomic/ionic photoabsorption parameters have been studied. Non -resonant photoionization in neon and argon isonuclear as well as isoelectronic sequences has been studied using a very sophisticated technique, namely the relativistic random phase approximation (RRPA). This technique takes into account relativistic effects as well as an important class of major many-body effects on the same footing. The present calculations confirmed that gross features of photoionization parameters calculated using simpler models were not an artifact of the simple model. Also, the present RRPA calculations on K^+ ion and neutral Ar brought out the relative importance of various many-body effects such the inter-channel coupling. Inter-channel coupling between discrete bound state photoexcitation channels from an inner atomic/ionic level and photoionization continuum channels from an outer atomic/ionic level leads to the phenomena of autoionization resonances in the photoionization process. These resonances lead to very complex effects in the atomic/ionic photoabsorption spectra. These resonances have been calculated and studied in the present work in the neon and magnesium isoelectronic sequences using the relativistic multi-channel quantum defect theory (RMQDT) within the framework of the RRPA. The

  19. The Kubo-Greenwood formula as a result of the random phase approximation for the electrons of the metal

    Science.gov (United States)

    Ivliev, S. V.

    2017-12-01

    For calculation of short laser pulse absorption in metal the imaginary part of permittivity, which is simply related to the conductivity, is required. Currently to find the static and dynamic conductivity the Kubo-Greenwood formula is most commonly used. It describes the electromagnetic energy absorption in the one-electron approach. In the present study, this formula is derived directly from the expression for the permittivity expression in the random phase approximation, which in fact is equivalent to the method of the mean field. The detailed analysis of the role of electron-electron interaction in the calculation of the matrix elements of the velocity operator is given. It is shown that in the one-electron random phase approximation the single-particle conductive electron wave functions in the field of fixed ions should be used. The possibility of considering the exchange and correlation effects by means of an amendment to a local function field is discussed.

  20. Model-Mapped RPA for Determining the Effective Coulomb Interaction

    Science.gov (United States)

    Sakakibara, Hirofumi; Jang, Seung Woo; Kino, Hiori; Han, Myung Joon; Kuroki, Kazuhiko; Kotani, Takao

    2017-04-01

    We present a new method to obtain a model Hamiltonian from first-principles calculations. The effective interaction contained in the model is determined on the basis of random phase approximation (RPA). In contrast to previous methods such as projected RPA and constrained RPA (cRPA), the new method named "model-mapped RPA" takes into account the long-range part of the polarization effect to determine the effective interaction in the model. After discussing the problems of cRPA, we present the formulation of the model-mapped RPA, together with a numerical test for the single-band Hubbard model of HgBa2CuO4.

  1. Correlation energy functional within the GW -RPA: Exact forms, approximate forms, and challenges

    Science.gov (United States)

    Ismail-Beigi, Sohrab

    2010-05-01

    In principle, the Luttinger-Ward Green’s-function formalism allows one to compute simultaneously the total energy and the quasiparticle band structure of a many-body electronic system from first principles. We present approximate and exact expressions for the correlation energy within the GW -random-phase approximation that are more amenable to computation and allow for developing efficient approximations to the self-energy operator and correlation energy. The exact form is a sum over differences between plasmon and interband energies. The approximate forms are based on summing over screened interband transitions. We also demonstrate that blind extremization of such functionals leads to unphysical results: imposing physical constraints on the allowed solutions (Green’s functions) is necessary. Finally, we present some relevant numerical results for atomic systems.

  2. Electric dipole strength and dipole polarizability in 48Ca within a fully self-consistent second random-phase approximation

    Science.gov (United States)

    Gambacurta, D.; Grasso, M.; Vasseur, O.

    2018-02-01

    The second random-phase-approximation model corrected by a subtraction procedure designed to cure double counting, instabilities, and ultraviolet divergences, is employed for the first time to analyze the dipole strength and polarizability in 48Ca. All the terms of the residual interaction are included, leading to a fully self-consistent scheme. Results are illustrated with two Skyrme parametrizations, SGII and SLy4. Those obtained with the SGII interaction are particularly satisfactory. In this case, the low-lying strength below the neutron threshold is well reproduced and the giant dipole resonance is described in a very satisfactory way especially in its spreading and fragmentation. Spreading and fragmentation are produced in a natural way within such a theoretical model by the coupling of 1 particle-1 hole and 2 particle-2 hole configurations. Owing to this feature, we may provide for the electric polarizability as a function of the excitation energy a curve with a similar slope around the centroid energy of the giant resonance compared to the corresponding experimental results. This represents a considerable improvement with respect to previous theoretical predictions obtained with the random-phase approximation or with several ab-initio models. In such cases, the spreading width of the excitation cannot be reproduced and the polarizability as a function of the excitation energy displays a stiff increase around the predicted centroid energy of the giant resonance.

  3. Coincidence: Fortran code for calculation of (e, e'x) differential cross-sections, nuclear structure functions and polarization asymmetry in self-consistent random phase approximation with Skyrme interaction

    Energy Technology Data Exchange (ETDEWEB)

    Cavinato, M.; Marangoni, M.; Saruis, A.M.

    1990-10-01

    This report describes the COINCIDENCE code written for the IBM 3090/300E computer in Fortran 77 language. The output data of this code are the (e, e'x) threefold differential cross-sections, the nuclear structure functions, the polarization asymmetry and the angular correlation coefficients. In the real photon limit, the output data are the angular distributions for plane polarized incident photons. The code reads from tape the transition matrix elements previously calculated, by in continuum self-consistent RPA (random phase approximation) theory with Skyrme interactions. This code has been used to perform a numerical analysis of coincidence (e, e'x) reactions with polarized electrons on the /sup 16/O nucleous.

  4. Lattice energies of molecular solids from the random phase approximation with singles corrections

    Czech Academy of Sciences Publication Activity Database

    Klimeš, Jiří

    2016-01-01

    Roč. 145, č. 9 (2016), 094506 ISSN 0021-9606 EU Projects: European Commission(XE) 658705 - NEW4NEW Grant - others:GA MŠk(CZ) LM2010005 Institutional support: RVO:61388955 Keywords : Approximation algorithms * Bins * Hydrogen bonds Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.965, year: 2016

  5. RPA correlations and nuclear densities in relativistic mean field approach

    International Nuclear Information System (INIS)

    Van Giai, N.; Liang, H.Z.; Meng, J.

    2007-02-01

    The relativistic mean field approach (RMF) is well known for describing accurately binding energies and nucleon distributions in atomic nuclei throughout the nuclear chart. The random phase approximation (RPA) built on top of the RMF is also a good framework for the study of nuclear excitations. Here, we examine the consequences of long range correlations brought about by the RPA on the neutron and proton densities as given by the RMF approach. (authors)

  6. Continuum random-phase approximation study of the incoherent μ--e- conversion rate and its spurious 1- admixture

    International Nuclear Information System (INIS)

    Papakonstantinou, P.; Wambach, J.; Kosmas, T.S.; Faessler, A.

    2006-01-01

    The incoherent transition strength of the exotic μ - -e - conversion in the 208 Pb nucleus is investigated by utilizing the continuum random-phase-approximation method, appropriate for the evaluation of the rate that goes to the continuum of the nuclear spectrum. We find that the contribution of resonances lying high in the continuum is not negligible. Special attention is paid to the detailed study of the pronounced 1 - contribution that according to previous calculations, dominates the overall incoherent rate in about all the nuclear targets. The spurious center-of-mass admixture to the partial rate originating from the 1 - excitations is explored, and its elimination is performed by correcting properly the dipole operators. The results found this way show that the greatest portion of the total 1 - contribution to the incoherent rate is spurious

  7. Lowest lying 2+ and 3- vibrational states in Pb, Sn, and Ni isotopes in relativistic quasiparticle random-phase approximation

    International Nuclear Information System (INIS)

    Ansari, A.; Ring, P.

    2006-01-01

    The excitation energies and electric multipole decay rates of the lowest lying 2 + and 3 - vibrational states in Pb, Sn, and Ni nuclei are calculated following relativistic quasiparticle random-phase approximation formalism based on the relativistic Hartree-Bogoliubov mean field. Two sets of Lagrangian parameters, NL1 and NL3, are used to investigate the effect of the nuclear force. Overall there is good agreement with the available experimental data for a wide range of mass numbers considered here, and the NL3 set seems to be a better choice. However, strictly speaking, these studies point toward the need of a new set of force parameters that could produce more realistic single-particle levels, at least in vicinity of the Fermi surface, of a wide range of nuclear masses

  8. Description of excited states in the nucleus using the Quasiparticle Random-Phase Approximation and the Gogny interaction

    International Nuclear Information System (INIS)

    Lechaftois, Francois

    2016-01-01

    This thesis presents three aspects centered around the QRPA (Quasiparticle Random Phase Approximation). The first consists in the use of an axial code to confront computed data with experimental results and to feed a microscopic reaction code. This step is a chance to analyse low-energy spectroscopy (few tens of MeV) of some nuclei, and more precisely (but not exclusively) the tin isotopic chain (Z=50). The second one relies on the improvement of the formalism to calculate multipolar electromagnetic transition operators, and a method to consolidate the computation of these operators, allowing to ease the programming by unifying the code for different multipolarities. Finally, in order to overcome the axial symmetry constraint, a new triaxial code has been developed. Its assets and development are presented, followed by the first batch of results. (author) [fr

  9. Random-phase-approximation approach to optical and magnetic excitations in the two-dimensional multiband Hubbard model

    International Nuclear Information System (INIS)

    Yonemitsu, K.; Bishop, A.R.

    1992-01-01

    As a convenient qualitative approach to strongly correlated electronic systems, an inhomogeneous Hartree-Fock plus random-phase approximation is applied to response functions for the two-dimensional multiband Hubbard model for cuprate superconductors. A comparison of the results with those obtained by exact diagonalization by Wagner, Hanke, and Scalapino [Phys. Rev. B 43, 10 517 (1991)] shows that overall structures in optical and magnetic particle-hole excitation spectra are well reproduced by this method. This approach is computationally simple, retains conceptual clarity, and can be calibrated by comparison with exact results on small systems. Most importantly, it is easily extended to larger systems and straightforward to incorporate additional terms in the Hamiltonian, such as electron-phonon interactions, which may play a crucial role in high-temperature superconductivity

  10. Randomized Phase II Trial of High-Dose Melatonin and Radiation Therapy for RPA Class 2 Patients With Brain Metastases (RTOG 0119)

    International Nuclear Information System (INIS)

    Berk, Lawrence; Berkey, Brian; Rich, Tyvin; Hrushesky, William; Blask, David; Gallagher, Michael; Kudrimoti, Mahesh; McGarry, Ronald C.; Suh, John; Mehta, Minesh

    2007-01-01

    Purpose: To determine if high-dose melatonin for Radiation Therapy Oncology Group (RTOG) recursive partitioning analysis (RPA) Class 2 patients with brain metastases improved survival over historical controls, and to determine if the time of day melatonin was given affected its toxicity or efficacy. RTOG 0119 was a phase II randomized trial for this group of patients. Methods and Materials: RTOG RPA Class 2 patients with brain metastases were randomized to 20 mg of melatonin, given either in the morning (8-9 AM) or in the evening (8-9 PM). All patients received radiation therapy (30 Gy in 10 fractions) in the afternoon. Melatonin was continued until neurologic deterioration or death. The primary endpoint was overall survival time. Neurologic deterioration, as reflected by the Mini-Mental Status Examination, was also measured. Results: Neither of the randomized groups had survival distributions that differed significantly from the historic controls of patients treated with whole-brain radiotherapy. The median survivals of the morning and evening melatonin treatments were 3.4 and 2.8 months, while the RTOG historical control survival was 4.1 months. Conclusions: High-dose melatonin did not show any beneficial effect in this group of patients

  11. Imaginary eigenvalue solution in RPA and phase transition

    International Nuclear Information System (INIS)

    Yao Yujie; Jing Xiaogong; Zhao Guoquan; Wu Shishu

    1993-01-01

    The phase transition (PT) of a many-particle system with a close-shell configuration, the stability of the Hartree-Fock (HF) solution and the random phase approximation (RPA) are studied by means of a generalized three-level solvable model. The question whether the occurrence of an imaginary eigenvalue solution in RPA (OISA) may be considered as a signature of PT is explored in some detail. It is found that there is no close relation between OISA and PT. Generally, OISA shows that RPA becomes poor

  12. Plasmon response in K, Na and Li clusters: systematics using the separable random-phase approximation with pseudo-Hamiltonians

    International Nuclear Information System (INIS)

    Kleinig, W.; Nesterenko, V.O.; Reinhard, P.-G.; Serra, Ll.

    1998-01-01

    The systematics of the plasmon response in spherical K, Na and Li clusters in a wide size region (8≤N≤440) is studied. We have considered two simplifying approximations whose validity has been established previously. First, a separable approach to the random-phase approximation is used. This involves an expansion of the residual interaction into a sum of separable terms until convergence is reached. Second, the electron-ion interaction is modelled by using the pseudo-Hamiltonian jellium model (MHJM) which includes nonlocal effects by means of realistic atomic pseudo-Hamiltonians. In cases where nonlocal effects are negligible the Structure Averaged Jellium Model (SAJM) has been used. Good agreement with available experimental data is achieved for K, Na (using the SAJM) and small Li clusters (invoking the PHJM). The trends for peak position and width are generally well reproduced, even up to details of the Landau fragmentation in several clusters. Less good agreement, however, is found for large Li clusters. This remains an open question

  13. Molecular Excitation Energies from Time-Dependent Density Functional Theory Employing Random-Phase Approximation Hessians with Exact Exchange.

    Science.gov (United States)

    Heßelmann, Andreas

    2015-04-14

    Molecular excitation energies have been calculated with time-dependent density-functional theory (TDDFT) using random-phase approximation Hessians augmented with exact exchange contributions in various orders. It has been observed that this approach yields fairly accurate local valence excitations if combined with accurate asymptotically corrected exchange-correlation potentials used in the ground-state Kohn-Sham calculations. The inclusion of long-range particle-particle with hole-hole interactions in the kernel leads to errors of 0.14 eV only for the lowest excitations of a selection of three alkene, three carbonyl, and five azabenzene molecules, thus surpassing the accuracy of a number of common TDDFT and even some wave function correlation methods. In the case of long-range charge-transfer excitations, the method typically underestimates accurate reference excitation energies by 8% on average, which is better than with standard hybrid-GGA functionals but worse compared to range-separated functional approximations.

  14. Inclusive charged-current neutrino-nucleus reactions calculated with the relativistic quasiparticle random-phase approximation

    International Nuclear Information System (INIS)

    Paar, N.; Vretenar, D.; Marketin, T.; Ring, P.

    2008-01-01

    Inclusive neutrino-nucleus cross sections are calculated using a consistent relativistic mean-field theoretical framework. The weak lepton-hadron interaction is expressed in the standard current-current form, the nuclear ground state is described with the relativistic Hartree-Bogoliubov model, and the relevant transitions to excited nuclear states are calculated in the relativistic quasiparticle random-phase approximation. Illustrative test calculations are performed for charged-current neutrino reactions on 12 C, 16 O, 56 Fe, and 208 Pb, and results compared with previous studies and available data. Through the use of the experimental neutrino fluxes, the averaged cross sections are evaluated for nuclei of interest for neutrino detectors. We analyze the total neutrino-nucleus cross sections and the evolution of the contribution of the different multipole excitations as a function of neutrino energy. The cross sections for reactions of supernova neutrinos on 16 O and 208 Pb target nuclei are analyzed as functions of the temperature and chemical potential

  15. Spin-adapted open-shell random phase approximation and time-dependent density functional theory. I. Theory.

    Science.gov (United States)

    Li, Zhendong; Liu, Wenjian

    2010-08-14

    The spin-adaptation of single-reference quantum chemical methods for excited states of open-shell systems has been nontrivial. The primary reason is that the configuration space, generated by a truncated rank of excitations from only one component of a reference multiplet, is spin-incomplete. Those "missing" configurations are of higher ranks and can, in principle, be recaptured by a particular class of excitation operators. However, the resulting formalisms are then quite involved and there are situations [e.g., time-dependent density functional theory (TD-DFT) under the adiabatic approximation] that prevent one from doing so. To solve this issue, we propose here a tensor-coupling scheme that invokes all the components of a reference multiplet (i.e., a tensor reference) rather than increases the excitation ranks. A minimal spin-adapted n-tuply excited configuration space can readily be constructed by tensor products between the n-tuple tensor excitation operators and the chosen tensor reference. Further combined with the tensor equation-of-motion formalism, very compact expressions for excitation energies can be obtained. As a first application of this general idea, a spin-adapted open-shell random phase approximation is first developed. The so-called "translation rule" is then adopted to formulate a spin-adapted, restricted open-shell Kohn-Sham (ROKS)-based TD-DFT (ROKS-TD-DFT). Here, a particular symmetry structure has to be imposed on the exchange-correlation kernel. While the standard ROKS-TD-DFT can access only excited states due to singlet-coupled single excitations, i.e., only some of the singly excited states of the same spin (S(i)) as the reference, the new scheme can capture all the excited states of spin S(i)-1, S(i), or S(i)+1 due to both singlet- and triplet-coupled single excitations. The actual implementation and computation are very much like the (spin-contaminated) unrestricted Kohn-Sham-based TD-DFT. It is also shown that spin-contaminated spin

  16. Short-range second order screened exchange correction to RPA correlation energies

    Science.gov (United States)

    Beuerle, Matthias; Ochsenfeld, Christian

    2017-11-01

    Direct random phase approximation (RPA) correlation energies have become increasingly popular as a post-Kohn-Sham correction, due to significant improvements over DFT calculations for properties such as long-range dispersion effects, which are problematic in conventional density functional theory. On the other hand, RPA still has various weaknesses, such as unsatisfactory results for non-isogyric processes. This can in parts be attributed to the self-correlation present in RPA correlation energies, leading to significant self-interaction errors. Therefore a variety of schemes have been devised to include exchange in the calculation of RPA correlation energies in order to correct this shortcoming. One of the most popular RPA plus exchange schemes is the second order screened exchange (SOSEX) correction. RPA + SOSEX delivers more accurate absolute correlation energies and also improves upon RPA for non-isogyric processes. On the other hand, RPA + SOSEX barrier heights are worse than those obtained from plain RPA calculations. To combine the benefits of RPA correlation energies and the SOSEX correction, we introduce a short-range RPA + SOSEX correction. Proof of concept calculations and benchmarks showing the advantages of our method are presented.

  17. Time-dependent Gross-Pitaevskii equation for composite bosons as the strong-coupling limit of the fermionic broken-symmetry random-phase approximation

    International Nuclear Information System (INIS)

    Strinati, G.C.; Pieri, P.

    2004-01-01

    The linear response to a space- and time-dependent external disturbance of a system of dilute condensed composite bosons at zero temperature, as obtained from the linearized version of the time-dependent Gross-Pitaevskii equation, is shown to result also from the strong-coupling limit of the time-dependent BCS (or broken-symmetry random-phase) approximation for the constituent fermions subject to the same external disturbance. In this way, it is possible to connect excited-state properties of the bosonic and fermionic systems by placing the Gross-Pitaevskii equation in perspective with the corresponding fermionic approximations

  18. On the dynamics of polymer mixtures in solution using the RPA

    International Nuclear Information System (INIS)

    Benmouna, M.

    1989-09-01

    The dynamics of polymer mixtures and copolymers in solution is investigated using the Random Phase Approximation (RPA). It is shown that the known results for the intermediate scattering functions are recovered in the Rouse limit only. If hydrodynamic interaction is not negligible, a discrepancy appears. This discrepancy can be observed by combining static and dynamic scattering experiments. (author). 10 refs

  19. Self-consistent GW0 results for the electron gas: Fixed screened potential W0 within the random-phase approximation

    International Nuclear Information System (INIS)

    von Barth, U.; Holm, B.

    1996-01-01

    With the aim of properly understanding the basis for and the utility of many-body perturbation theory as applied to extended metallic systems, we have calculated the electronic self-energy of the homogeneous electron gas within the GW approximation. The calculation has been carried out in a self-consistent way; i.e., the one-electron Green function obtained from Dyson close-quote s equation is the same as that used to calculate the self-energy. The self-consistency is restricted in the sense that the screened interaction W is kept fixed and equal to that of the random-phase approximation for the gas. We have found that the final results are marginally affected by the broadening of the quasiparticles, and that their self-consistent energies are still close to their free-electron counterparts as they are in non-self-consistent calculations. The reduction in strength of the quasiparticles and the development of satellite structure (plasmons) gives, however, a markedly smaller dynamical self-energy leading to, e.g., a smaller reduction in the quasiparticle strength as compared to non-self-consistent results. The relatively bad description of plasmon structure within the non-self-consistent GW approximation is marginally improved. A first attempt at including W in the self-consistency cycle leads to an even broader and structureless satellite spectrum in disagreement with experiment. copyright 1996 The American Physical Society

  20. Combinations of coupled cluster, density functionals, and the random phase approximation for describing static and dynamic correlation, and van der Waals interactions

    Science.gov (United States)

    Garza, Alejandro J.; Bulik, Ireneusz W.; Alencar, Ana G. Sousa; Sun, Jianwei; Perdew, John P.; Scuseria, Gustavo E.

    2016-04-01

    Contrary to standard coupled cluster doubles (CCD) and Brueckner doubles (BD), singlet-paired analogues of CCD and BD (denoted here as CCD0 and BD0) do not break down when static correlation is present, but neglect substantial amounts of dynamic correlation. In fact, CCD0 and BD0 do not account for any contributions from multielectron excitations involving only same-spin electrons at all. We exploit this feature to add - without introducing double counting, self-interaction, or increase in cost - the missing correlation to these methods via meta-GGA (generalised gradient approximation) density functionals (Tao-Perdew-Staroverov-Scuseria and strongly constrained and appropriately normed). Furthermore, we improve upon these CCD0+DFT blends by invoking range separation: the short- and long-range correlations absent in CCD0/BD0 are evaluated with density functional theory and the direct random phase approximation, respectively. This corrects the description of long-range van der Waals forces. Comprehensive benchmarking shows that the combinations presented here are very accurate for weakly correlated systems, while also providing a reasonable description of strongly correlated problems without resorting to symmetry breaking.

  1. Self-consistent RPA calculations with Skyrme-type interactions: The skyrme_rpa program

    Science.gov (United States)

    Colò, Gianluca; Cao, Ligang; Van Giai, Nguyen; Capelli, Luigi

    2013-01-01

    Random Phase Approximation (RPA) calculations are nowadays an indispensable tool in nuclear physics studies. We present here a complete version implemented with Skyrme-type interactions, with the spherical symmetry assumption, that can be used in cases where the effects of pairing correlations and of deformation can be ignored. The full self-consistency between the Hartree-Fock mean field and the RPA excitations is enforced, and it is numerically controlled by comparison with energy-weighted sum rules. The main limitations are that charge-exchange excitations and transitions involving spin operators are not included in this version. Program summaryProgram title: skyrme_rpa (v 1.00) Catalogue identifier: AENF_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AENF_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 5531 No. of bytes in distributed program, including test data, etc.: 39435 Distribution format: tar.gz Programming language: FORTRAN-90/95; easily downgradable to FORTRAN-77. Computer: PC with Intel Celeron, Intel Pentium, AMD Athlon and Intel Core Duo processors. Operating system: Linux, Windows. RAM: From 4 MBytes to 150 MBytes, depending on the size of the nucleus and of the model space for RPA. Word size: The code is written with a prevalent use of double precision or REAL(8) variables; this assures 15 significant digits. Classification: 17.24. Nature of problem: Systematic observations of excitation properties in finite nuclear systems can lead to improved knowledge of the nuclear matter equation of state as well as a better understanding of the effective interaction in the medium. This is the case of the nuclear giant resonances and low-lying collective excitations, which can be described as small amplitude collective motions in the framework of

  2. Partial restoration of spin-isospin SU(4) symmetry and the one-quasiparticle random-phase approximation method in double-β decay

    Science.gov (United States)

    Ferreira, V. dos S.; Krmpotić, F.; Barbero, C. A.; Samana, A. R.

    2017-10-01

    The one-quasiparticle random-phase approximation (one-QRPA) method is used to describe simultaneously both double-β -decay modes, giving special attention to the partial restoration of spin-isospin SU(4 ) symmetry. To implement this restoration and to fix the model parameters, we resort to the energetics of Gamow-Teller resonances and to the minima of the single-β+-decay strengths. This makes the theory predictive regarding the β β2 ν decay, producing the 2 ν moments in 48Ca, 76Ge, 82Se, 96Zr, 100Mo, Te,130128, and 150Nd, that are of the same order of magnitude as the experimental ones; however, the agreement with β β2 ν data is only modest. To include contributions coming from induced nuclear weak currents, we extend the β β0 ν -decay formalism employed previously in C. Barbero et al., Nucl. Phys. A 628, 170 (1998), 10.1016/S0375-9474(97)00614-3, which is based on the Fourier-Bessel expansion. The numerical results for the β β0 ν moments in the above mentioned nuclei are similar to those obtained in other theoretical studies although smaller on average by ˜40 % . We attribute this difference basically to the one-QRPA method, employed here for the first time, instead of the currently used two-QRPA method. The difference is partially due also to the way of carrying out the restoration of the spin-isospin symmetry. It is hard to say which is the best way to make this restoration, since the β β0 ν moments are not experimentally measurable. The recipe proposed here is based on physically robust arguments. The numerical uncertainties in the β β moments, related to (i) their strong dependence on the residual interaction in the particle-particle channel when evaluated within the QRPA, and (ii) lack of proper knowledge of single-particle energies, have been quantified. It is concluded that the partial restoration of the SU(4 ) symmetry, generated by the residual interaction, is crucial in the description of the β β decays, regardless of the nuclear

  3. On the role of anti-bound states in the RPA description of the giant monopole resonance

    International Nuclear Information System (INIS)

    Vertse, T.; Bang, J.

    1989-01-01

    The limit of the applicability of the resonant Random Phase Approximation (RPA) method is tested by calculating escape widths in the giant monopole resonance of 16 O and comparing them to the results of a time dependent Hartree-Fock calculation. Though the widths of the narrow s-wave component agree reasonably well, the broad p-wave component shows large disagreement, which cannot be cured by complementing the basis with anti-bound states in the RPA calculation. (author) 18 refs.; 3 tabs

  4. RPA correction to the optical potential

    Directory of Open Access Journals (Sweden)

    Bauge E.

    2010-03-01

    Full Text Available In studies of nucleon elastic scattering, a correction to the microscopic optical potential built from Melbourne g-matrix was found to be necessary at low nucleon incident energy [1,2]. Indeed, at energies lower than 60 MeV, the absorption generated from Melbourne g-matrix is too weak within 25%. Coupling to collective excited states of the target nucleus are not included in the g-matrix and could explain the missing absorption. We propose to calculate this correction to the optical potential using the Gogny D1S effective nucleon-nucleon interaction in the coupling to excited states of the target. We use the Random Phase Approximation (RPA description of the excited states of the target with the same interaction.

  5. Application of the RPA method based on the cranked Hartree-Fock-Bogolyubov model in 168Er and 158Dy

    International Nuclear Information System (INIS)

    Kvasil, J.; Khariev, M.M.; Cwiok, S.; Mikhajlov, I.N.; Khoriev, B.

    1984-01-01

    The Random Phase Approximation (RPA) based on the Cranked Hartree-Fock-Bogolyubov (CHFB) model is used for the study of low-lying nuclear states near the yrast line in 158 Dy and 168 Er. The relation of the spurious unphysical states connected with the nucleus centre of mass rotational motion to the solutions of RPA equations of motion is cleared up. The calculated level energies and reduced probabilities B(E2) are compared with experimental ones. The dependence of the residual interaction strength constants and the nucleus moment of inertia on the angular momentum is discussed. The experimental characteristics of low-lying states up to approx. 2 MeV are reproduced by the CHFB+RPA model. (author)

  6. Second RPA calculations with the Skyrme and Gogny interactions

    Energy Technology Data Exchange (ETDEWEB)

    Gambacurta, Danilo [Horia Hulubei National Institute for Physics and Nuclear Engineering, Extreme Light Infrastructure - Nuclear Physics (ELI-NP), Magurele, Jud. Ilfov (Romania); Grasso, Marcella [Universite Paris-Sud, IN2P3-CNRS, Institut de Physique Nucleaire, Orsay Cedex (France)

    2016-07-15

    The Second Random Phase Approximation (SRPA) is a natural extension of RPA where more general excitation operators are introduced. These operators contain, in addition to the one particle-one hole configurations already considered in RPA, also two particle-two hole excitations. Only in the last years, large-scale SRPA calculations have been performed, showing the merits and limits of this approach. In the first part of this paper, we present an overview of recent applications of the SRPA based on the Skyrme and Gogny interactions. Giant resonances in {sup 16}O will be studied and their properties discussed by using different models. In particular, we will present the first applications of the SRPA model with the finite-range Gogny interaction, discussing the advantages and drawbacks of using such an interaction in this type of calculations. After that, some more recent results, obtained by using a subtraction procedure to overcome double-counting in the SRPA, will be discussed. We will show that this procedure leads to results that are weakly cutoff dependent and that a strong reduction of the SRPA downwards shift with respect to the RPA spectra is found. Moreover, applying this procedure for the first time in the Gogny-SRPA framework, we will show that this method is able to reduce the anomalous shift found in previous calculations and related to some proton-neutron matrix elements of the residual interaction. (orig.)

  7. RPA method based on the self-consistent cranking model for 168Er and 158Dy

    International Nuclear Information System (INIS)

    Kvasil, J.; Cwiok, S.; Chariev, M.M.; Choriev, B.

    1983-01-01

    The low-lying nuclear states in 168 Er and 158 Dy are analysed within the random phase approximation (RPA) method based on the self-consistent cranking model (SCCM). The moment of inertia, the value of chemical potential, and the strength constant k 1 have been obtained from the symmetry condition. The pairing strength constants Gsub(tau) have been determined from the experimental values of neutron and proton pairing energies for nonrotating nuclei. A quite good agreement with experimental energies of states with positive parity was obtained without introducing the two-phonon vibrational states

  8. The second-order polarization propagator approximation (SOPPA) method coupled to the polarizable continuum model

    DEFF Research Database (Denmark)

    Eriksen, Janus Juul; Solanko, Lukasz Michal; Nåbo, Lina J.

    2014-01-01

    2) wave function coupled to PCM, we introduce dynamical PCM solvent effects only in the Random Phase Approximation (RPA) part of the SOPPA response equations while the static solvent contribution is kept in both the RPA terms as well as in the higher order correlation matrix components of the SOPPA...... response equations. By dynamic terms, we refer to contributions that describe a change in environmental polarization which, in turn, reflects a change in the core molecular charge distribution upon an electronic excitation. This new combination of methods is termed PCM-SOPPA/RPA. We apply this newly...... defined method to the challenging cases of solvent effects on the lowest and intense electronic transitions in o-, m- and p-nitroaniline and o-, m- and p-nitrophenol and compare the performance of PCM-SOPPA/RPA with more conventional approaches. Compared to calculations based on time-dependent density...

  9. γ-decay of {}_{8}^{16}{{\\rm{O}}}_{8}\\,{and}\\,{}_{7}^{16}{{\\rm{N}}}_{9} in proton-neutron Tamm-Dancoff and random phase approximations with optimized surface δ interaction

    Science.gov (United States)

    Pahlavani, M. R.; Firoozi, B.

    2016-09-01

    γ-ray transitions from excited states of {}16{{N}} and {}16{{O}} isomers that appear in the γ spectrum of the {}616{{{C}}}10\\to {}716{{{N}}}9\\to {}816{{{O}}}8 beta decay chain are investigated. The theoretical approach used in this research starts with a mean-field potential consisting of a phenomenological Woods-Saxon potential including spin-orbit and Coulomb terms (for protons) in order to obtain single-particle energies and wave functions for nucleons in a nucleus. A schematic residual surface delta interaction is then employed on the top of the mean field and is treated within the proton-neutron Tamm-Dancoff approximation (pnTDA) and the proton-neutron random phase approximation. The goal is to use an optimized surface delta interaction interaction, as a residual interaction, to improve the results. We have used artificial intelligence algorithms to establish a good agreement between theoretical and experimental energy spectra. The final results of the ‘optimized’ calculations are reasonable via this approach.

  10. Electron - A fortran programme for the coupled channel calculation of nuclear electromagnetic (e,e') form factors and cross sections in the self-consistent random-phase approximation

    International Nuclear Information System (INIS)

    Cavinato, M.; Marangoni, M.; Saruis, A.M.

    1984-01-01

    Description is given of the Electron programme for IBM 370/168 computer, written in Fortran 4. language. The programme calculates (e,e') cross-sections and longitudinal/transverse form factors for closed shell nuclei in the framework of a self-consistent RPA theory

  11. Description of the 2ν ββ decay within a fully-renormalized RPA approach

    International Nuclear Information System (INIS)

    Raduta, A. A.; Raduta, C. M.; Faessler, A.; Kaminski, W. K.

    1998-01-01

    The RPA treatment of a many body Hamiltonian describing the states of even-even nuclei involved in a 2νββ decay is revisited. One shows that re-normalizing the dipole two quasiparticle operators by accounting for new correlations in the ground state requires a similar re-normalization for the dipole density operators which results in activating new boson degrees of freedom. Possible consequences on Ikeda sum rule and Gamow-Teller (GT) transition amplitude are suggested. A numerical application for a two levels model is presented. The present formalism is hereafter referred to as the frn RPA (full re-normalised Random Phase Approximation). The equations for the new RPA amplitudes and energies were analytically derived. The solutions having the new terms amplitudes dominant define a new proton-neutron dipole mode. It is proved that the new mode appears as a result of a partial restoration of the Pauli principle. The QRPA equations and the equations defining the averages of the quasiparticle number operators are to be self consistently solved by an iterative procedure. Within the new QRPA procedure analytical formulae for the Ikeda sum rule and the GT transition amplitude were derived. The frn RPA has been applied to the case of a single level for protons and a single level for neutrons. The frn RPA equations exhibit two solutions, the lower one characterizing the new mode, i.e. that whose maximum amplitude is Z. Although the other mode has an energy higher than the energies provided by the standard and the rn RPA approaches, the frn RPA breaks down before the normal RPA and this happens due to the collapse of the new mode. Before the frn RPA breaks down the GT transition amplitude vanishes. In the new approach the Ikeda sum rule is reasonably well reproduced. Comparing the results of the present approach with those of the rn RPA it is worth enumerating the contrasting features. I) a) The rn RPA exhibits the beauty of avoiding the collapse of the mode energy. b

  12. The nature of excess electrons in anatase and rutile from hybrid DFT and RPA.

    Science.gov (United States)

    Spreafico, Clelia; VandeVondele, Joost

    2014-12-21

    The behavior of excess electrons in undoped and defect free bulk anatase and rutile TiO2 has been investigated by state-of-the-art electronic structure methods including hybrid density functional theory (DFT) and the random phase approximation (RPA). Consistent with experiment, charge trapping and polaron formation is observed in both anatase and rutile. The difference in the anisotropic shape of the polarons is characterized, confirming for anatase the large polaron picture. For anatase, where polaron formation energies are small, charge trapping is observed also with standard hybrid functionals, provided the simulation cell is sufficiently large (864 atoms) to accommodate the lattice relaxation. Even though hybrid orbitals are required as a starting point for RPA in this system, the obtained polaron formation energies are relatively insensitive to the amount of Hartree-Fock exchange employed. The difference in trapping energy between rutile and anatase can be obtained accurately with both hybrid functionals and RPA. Computed activation energies for polaron hopping and delocalization clearly show that anatase and rutile might have different charge transport mechanisms. In rutile, only hopping is likely, whereas in anatase hopping and delocalization are competing. Delocalization will result in conduction-band-like and thus enhanced transport. Anisotropic conduction, in agreement with experimental data, is observed, and results from the tendency to delocalize in the [001] direction in rutile and the (001) plane in anatase. For future work, our calculations serve as a benchmark and suggest RPA on top on hybrid orbitals (PBE0 with 30% Hartree-Fock exchange), as a suitable method to study the rich chemistry and physics of TiO2.

  13. Finite rank separable approximation for Skyrme interactions: spin-isospin excitations

    International Nuclear Information System (INIS)

    Severyukhin, A.P.; Voronov, V.V.; Borzov, I.N.; Nguyen Van Giai

    2012-01-01

    A finite rank separable approximation for the quasiparticle random phase approximation with the Skyrme interactions is applied for the case of charge-exchange nuclear modes. The coupling between one- and two-phonon terms in the wave functions is taken into account. It has been shown that the approximation reproduces reasonably well the full charge-exchange RPA results for the spin-dipole resonances in 132 Sn. As an illustration of the method, the phonon-phonon coupling effect on the β-decay half-life of 78 Ni is considered

  14. Replication Protein A (RPA) Phosphorylation Prevents RPA Association with Replication Centers

    OpenAIRE

    Vassin, Vitaly M.; Wold, Marc S.; Borowiec, James A.

    2004-01-01

    Mammalian replication protein A (RPA) undergoes DNA damage-dependent phosphorylation at numerous sites on the N terminus of the RPA2 subunit. To understand the functional significance of RPA phosphorylation, we expressed RPA2 variants in which the phosphorylation sites were converted to aspartate (RPA2D) or alanine (RPA2A). Although RPA2D was incorporated into RPA heterotrimers and supported simian virus 40 DNA replication in vitro, the RPA2D mutant was selectively unable to associate with re...

  15. Electroexcitation of Low-Lying Particle-Hole RPA States of 16O with WBP Interaction

    International Nuclear Information System (INIS)

    Taqi, Ali H.; Radhi, R.A.; Hussein, Adil M.

    2014-01-01

    The nuclear structure of 16 O is studied in the framework of the particle-hole random phase approximation (ph RPA). The Hamiltonian is diagonalized within a model space with particle orbits {1d 5/2 ,1d 3/2 , and 2s 1/2 } and the hole orbits {1p 3/2 and 1p 1/2 } using Warburton and Brown interaction WBP. The ph RPA calculations are tested, by comparing the electron scattering form factors with the available experimental data. The results of electron scattering form factors and reduced transition strength for the states: 1 − , T = 0 (7.116 MeV); 2 − , T = 1 (12.968 MeV); 2 − , T = 1 (20.412 MeV); and 3 − , T = 0 (6.129 MeV) are interpreted in terms of the harmonic-oscillator (HO) wave functions of size parameter b. The occupation probabilities of the single particle and hole orbits are calculated. The spurious states are removed by adding the center of mass (CM) correction to the nuclear Hamiltonian. A comparison with the available experiments data is presented. (nuclear physics)

  16. Electroexcitation of Low-Lying Particle-Hole RPA States of 16O with WBP Interaction

    Science.gov (United States)

    Ali, H. Taqi; R. A., Radhi; Adil, M. Hussein

    2014-12-01

    The nuclear structure of 16O is studied in the framework of the particle-hole random phase approximation (ph RPA). The Hamiltonian is diagonalized within a model space with particle orbits {1d5/2,1d3/2, and 2s1/2} and the hole orbits {1p3/2 and 1p1/2} using Warburton and Brown interaction WBP. The ph RPA calculations are tested, by comparing the electron scattering form factors with the available experimental data. The results of electron scattering form factors and reduced transition strength for the states: 1-, T = 0 (7.116 MeV); 2-, T = 1 (12.968 MeV); 2-, T = 1 (20.412 MeV); and 3-, T = 0 (6.129 MeV) are interpreted in terms of the harmonic-oscillator (HO) wave functions of size parameter b. The occupation probabilities of the single particle and hole orbits are calculated. The spurious states are removed by adding the center of mass (CM) correction to the nuclear Hamiltonian. A comparison with the available experiments data is presented.

  17. Nuclear response in an extended RPA formalism; an application to 48Ca

    International Nuclear Information System (INIS)

    Brand, M.G.E.; Allaart, K.; Dickhoff, W.H.

    1990-01-01

    An extension of the standard (1p1h) Random Phase Approximation (RPA) is derived, by considering the Feynman diagram expansion of the polarization propagator and the relationship between the self-energy and the particle-hole interaction that must be fulfilled in order to obey conservation laws. The resulting Extended RPA (ERPA) equations include the dynamic coupling of 1p1h states to 2p2h states, which leads to a fragmentation of single-particle and single-hole strength and screening of the interaction by the medium. The method has been applied to 48 Ca using a realistic G-matrix interaction based on meson-exchange. The results show an improved description of the response over the whole energy range up to 100 MeV. Remaining discrepancies point in the direction of further strength reduction due to short-range correlations as well as a stronger coupling to 2p2h states at low energy. (author)

  18. Superfluid and insulating phases in an interacting-boson model: mean-field theory and the RPA

    International Nuclear Information System (INIS)

    Sheshadri, K.; Pandit, R.; Krishnamurthy, H.R.; Ramakrishnan, T.V.

    1993-01-01

    The bosonic Hubbard model is studied via a simple mean-field theory. At zero temperature, in addition to yielding a phase diagram that is qualitatively correct, namely a superfluid phase for non-integer fillings and a Mott transition from a superfluid to an insulating phase for integer fillings, this theory gives results that are in good agreement with Monte Carlo simulations. In particular, the superfluid fraction obtained as a function of the interaction strength U for both integer and non-integer fillings is close to the simulation results. In all phases the excitation spectra are obtained by using the random phase approximation (RPA): the spectrum has a gap in the insulating phase and is gapless (and linear at small wave vectors) in the superfluid phase. Analytic results are presented in the limits of large U and small superfluid density. Finite-temperature phase diagrams and the Mott-insulator-normal-phase crossover are also described. (orig.)

  19. Effective nucleon-nucleon interaction in the RPA

    International Nuclear Information System (INIS)

    Batista, E.F.; Carlson, B.V.; Conti, C. de; Frederico, T.

    2001-01-01

    The purpose of the present work is to study the properties of the effective nucleon-nucleon interaction, in a infinite system of mesons and baryons , using the relativistic Hartree-Fock-Bogoliubov approximation. To derive the RHFB equations in a systematic fashion, we use Dyson's equation to sum to all orders the self-consistent tadpole and exchange contributions to the extended baryon Green's function (the Gorkov propagator). The meson propagator is computed as a sum over ring diagrams which consist in repeated insertions of the lowest-order proper polarization graph. The sum is the diagrammatic equivalent of the relativistic random phase approximation (RPA) that describes the well-known collective modes. In the nuclear medium, the σ and ω propagators are linked because of scalar-vector mixing, a density-dependent effect that generates a coupling between the Dyson's equation for the meson propagators. We use the dressed meson propagator to obtain the effective interaction and investigate its effect on the 1 S 0 pairing in nuclear matter. The effective interaction has title effect on the self-energy mean field, since the latter is dominated by the Hartree contribution, which is determined by the free meson propagators. The pairing field, however, is obtained from an exchange term, in which the effective interaction can play an important role. As the polarization corrections to the meson propagators tend to increase the σ-meson mass and decrease the ω-meson mass, they result in an effective interaction which is more repulsive than the bare one. We would expect this to result in a decrease in the 1 S 0 pairing, similar to that seen in nonrelativistic calculations. (author)

  20. Toward a consistent RHA-RPA

    International Nuclear Information System (INIS)

    Shepard, J.R.

    1991-01-01

    The authors examine the RPA based on a relativistic Hartree approximation description for nuclear ground states. This model includes contributions from the negative energy sea at the 1-loop level. They emphasize consistency between the treatment of the ground state and the RPA. This consistency is important in the description of low-lying collective levels but less important for the longitudinal (e, e') quasi-elastic response. They also study the effect of imposing a 3-momentum cutoff on negative energy sea contributions. A cutoff of twice the nucleon mass improves agreement with observed spin orbit splittings in nuclei compared to the standard infinite cutoff results, an effect traceable to the fact that imposing the cutoff reduces m*/m. The cutoff is much less important than consistency in the description of low-lying collective levels. The cutoff model provides excellent agreement with quasi-elastic (e, e') data

  1. Quantal Brownian Motion from RPA dynamics: The master and Fokker-Planck equations

    International Nuclear Information System (INIS)

    Yannouleas, C.

    1984-05-01

    From the purely quantal RPA description of the damped harmonic oscillator and of the corresponding Brownian Motion within the full space (phonon subspace plus reservoir), a master equation (as well as a Fokker-Planck equation) for the reduced density matrix (for the reduced Wigner function, respectively) within the phonon subspace is extracted. The RPA master equation agrees with the master equation derived by the time-dependent perturbative approaches which utilize Tamm-Dancoff Hilbert spaces and invoke the rotating wave approximation. Since the RPA yields a full, as well as a contracted description, it can account for both the kinetic and the unperturbed oscillator momenta. The RPA description of the quantal Brownian Motion contrasts with the descriptions provided by the time perturbative approaches whether they invoke or not the rotating wave approximation. The RPA description also contrasts with the phenomenological phase space quantization. (orig.)

  2. The nuclear response in extended RPA theories

    International Nuclear Information System (INIS)

    Wambach, J.

    1991-01-01

    Linear response theories for small-amplitude nuclear motion are discussed. A review is given of the Random-Phase-Approximation and its successes and shortcomings are pointed out. Systematic improvements are presented which include two-particle two-hole excitations and account for dissipative effects due to binary collisions of nucleons in the mean field. These improved theories describe inelastic scattering experiments satisfactorily over a wide kinematical range. (author)

  3. Microscopic nuclear-dissipation mechanism as damping of collective motion in the second RPA

    International Nuclear Information System (INIS)

    Yannouleas, C.; Dworzecka, M.; Griffin, J.J.

    1982-01-01

    A microscopic model for the damping of the one-phonon RPA collective state, absolute value c > = Q/sub c/ 0 > /sub S//sub R/, has been previously described. This one-phonon RPA collective state is defined within a restricted subspace, S/sub R/, of the discrete 1p-1h structure. Its damping is described within an extended subspace, S = S/sub R/ + S/sub A/, by the time evolution of a wave packet according to the RPA and the Second RPA approximations of the complete Schroedinger equation when initialized with the one-phonon state. The one-phonon state, however, is unable to describe time-varying oscillations of the mean field. Such oscillations require wave packets formed by linear superposition of the RPA many-phonon eigenstates. Coherent time-varying oscillations of the mean field (multi-phonon initial states) are discussed

  4. RPA tree-level database users guide

    Science.gov (United States)

    Patrick D. Miles; Scott A. Pugh; Brad Smith; Sonja N. Oswalt

    2014-01-01

    The Forest and Rangeland Renewable Resources Planning Act (RPA) of 1974 calls for a periodic assessment of the Nation's renewable resources. The Forest Inventory and Analysis (FIA) program of the U.S. Forest Service supports the RPA effort by providing information on the forest resources of the United States. The RPA tree-level database (RPAtreeDB) was generated...

  5. Random-phase metasurfaces at optical wavelengths

    DEFF Research Database (Denmark)

    Pors, Anders; Ding, Fei; Chen, Yiting

    2016-01-01

    , with statistics obeying the theoretical predictions. We foresee the use of random-phase metasurfaces for camouflage applications and as high-quality reference structures in dark-field microscopy, while the control of the statistics for polarised and unpolarised light might find usage in security applications...

  6. RPA ground state correlations in nuclei

    International Nuclear Information System (INIS)

    Lenske, H.

    1990-01-01

    Overcounting in the RPA theory of ground state correlations is shown to be avoided if exact rather than quasiboson commutators are used. Single particle occupation probabilities are formulated in a compact way by the RPA Green function. Calculations with large configuration spaces and realistic interactions are performed with 1p1h RPA and second RPA (SRPA) including 2p2h mixing in excited states. In 41 Ca valence hole states are found to be quenched by about 10% in RPA and up to 18% in SRPA. Contributions from low and high lying excitations and their relation to long and short range correlations in finite nuclei are investigated. (orig.)

  7. Sum rules in extended RPA theories

    International Nuclear Information System (INIS)

    Adachi, S.; Lipparini, E.

    1988-01-01

    Different moments m k of the excitation strength function are studied in the framework of the second RPA and of the extended RPA in which 2p2h correlations are explicitly introduced into the ground state by using first-order perturbation theory. Formal properties of the equations of motion concerning sum rules are derived and compared with those exhibited by the usual 1p1h RPA. The problem of the separation of the spurious solutions in extended RPA calculations is also discussed. (orig.)

  8. Physical interaction between replication protein A (RPA) and MRN: involvement of RPA2 phosphorylation and the N-terminus of RPA1.

    Science.gov (United States)

    Oakley, Greg G; Tillison, Kristin; Opiyo, Stephen A; Glanzer, Jason G; Horn, Jeffrey M; Patrick, Steve M

    2009-08-11

    Replication protein A (RPA) is a heterotrimeric protein consisting of RPA1, RPA2, and RPA3 subunits that binds to single-stranded DNA (ssDNA) with high affinity. The response to replication stress requires the recruitment of RPA and the MRE11-RAD50-NBS1 (MRN) complex. RPA bound to ssDNA stabilizes stalled replication forks by recruiting checkpoint proteins involved in fork stabilization. MRN can bind DNA structures encountered at stalled or collapsed replication forks, such as ssDNA-double-stranded DNA (dsDNA) junctions or breaks, and promote the restart of DNA replication. Here, we demonstrate that RPA2 phosphorylation regulates the assembly of DNA damage-induced RPA and MRN foci. Using purified proteins, we observe a direct interaction between RPA with both NBS1 and MRE11. By utilizing RPA bound to ssDNA, we demonstrate that substituting RPA with phosphorylated RPA or a phosphomimetic weakens the interaction with the MRN complex. Also, the N-terminus of RPA1 is a critical component of the RPA-MRN protein-protein interaction. Deletion of the N-terminal oligonucleotide-oligosaccharide binding fold (OB-fold) of RPA1 abrogates interactions of RPA with MRN and individual proteins of the MRN complex. Further identification of residues critical for MRN binding in the N-terminus of RPA1 shows that substitution of Arg31 and Arg41 with alanines disrupts the RPA-MRN interaction and alters cell cycle progression in response to DNA damage. Thus, the N-terminus of RPA1 and phosphorylation of RPA2 regulate RPA-MRN interactions and are important in the response to DNA damage.

  9. Physical Interaction between Replication Protein A (RPA) and MRN: Involvement of RPA2 Phosphorylation and the N-terminus of RPA1

    OpenAIRE

    Oakley, Greg; Tillison, Kristin; Opiyo, Stephen; Glanzer, Jason; Horn, Jeffrey M.; Patrick, Steve M.

    2009-01-01

    Replication protein A (RPA) is a heterotrimeric protein consisting of RPA1, RPA2 and RPA3 subunits that binds to ssDNA with high affinity. The response to replication stress requires the recruitment of RPA and the MRE11/RAD50/NBS1 (MRN) complex. RPA bound to ssDNA stabilizes stalled replication forks by recruiting checkpoint proteins involved in fork stabilization. MRN can bind DNA structures encountered at stalled or collapsed replication forks, such as ssDNA-dsDNA junctions or breaks and pr...

  10. In vitro analysis of the role of replication protein A (RPA) and RPA phosphorylation in ATR-mediated checkpoint signaling.

    Science.gov (United States)

    Lindsey-Boltz, Laura A; Reardon, Joyce T; Wold, Marc S; Sancar, Aziz

    2012-10-19

    Replication protein A (RPA) plays essential roles in DNA metabolism, including replication, checkpoint, and repair. Recently, we described an in vitro system in which the phosphorylation of human Chk1 kinase by ATR (ataxia telangiectasia mutated and Rad3-related) is dependent on RPA bound to single-stranded DNA. Here, we report that phosphorylation of other ATR targets, p53 and Rad17, has the same requirements and that RPA is also phosphorylated in this system. At high p53 or Rad17 concentrations, RPA phosphorylation is inhibited and, in this system, RPA with phosphomimetic mutations cannot support ATR kinase function, whereas a non-phosphorylatable RPA mutant exhibits full activity. Phosphorylation of these ATR substrates depends on the recruitment of ATR and the substrates by RPA to the RPA-ssDNA complex. Finally, mutant RPAs lacking checkpoint function exhibit essentially normal activity in nucleotide excision repair, revealing RPA separation of function for checkpoint and excision repair.

  11. In Vitro Analysis of the Role of Replication Protein A (RPA) and RPA Phosphorylation in ATR-mediated Checkpoint Signaling*

    Science.gov (United States)

    Lindsey-Boltz, Laura A.; Reardon, Joyce T.; Wold, Marc S.; Sancar, Aziz

    2012-01-01

    Replication protein A (RPA) plays essential roles in DNA metabolism, including replication, checkpoint, and repair. Recently, we described an in vitro system in which the phosphorylation of human Chk1 kinase by ATR (ataxia telangiectasia mutated and Rad3-related) is dependent on RPA bound to single-stranded DNA. Here, we report that phosphorylation of other ATR targets, p53 and Rad17, has the same requirements and that RPA is also phosphorylated in this system. At high p53 or Rad17 concentrations, RPA phosphorylation is inhibited and, in this system, RPA with phosphomimetic mutations cannot support ATR kinase function, whereas a non-phosphorylatable RPA mutant exhibits full activity. Phosphorylation of these ATR substrates depends on the recruitment of ATR and the substrates by RPA to the RPA-ssDNA complex. Finally, mutant RPAs lacking checkpoint function exhibit essentially normal activity in nucleotide excision repair, revealing RPA separation of function for checkpoint and excision repair. PMID:22948311

  12. Review of Random Phase Encoding in Volume Holographic Storage

    Directory of Open Access Journals (Sweden)

    Wei-Chia Su

    2012-09-01

    Full Text Available Random phase encoding is a unique technique for volume hologram which can be applied to various applications such as holographic multiplexing storage, image encryption, and optical sensing. In this review article, we first review and discuss diffraction selectivity of random phase encoding in volume holograms, which is the most important parameter related to multiplexing capacity of volume holographic storage. We then review an image encryption system based on random phase encoding. The alignment of phase key for decryption of the encoded image stored in holographic memory is analyzed and discussed. In the latter part of the review, an all-optical sensing system implemented by random phase encoding and holographic interconnection is presented.

  13. HARP preferentially co-purifies with RPA bound to DNA-PK and blocks RPA phosphorylation.

    Science.gov (United States)

    Quan, Jinhua; Yusufzai, Timur

    2014-05-01

    The HepA-related protein (HARP/SMARCAL1) is an ATP-dependent annealing helicase that is capable of rewinding DNA structures that are stably unwound due to binding of the single-stranded DNA (ssDNA)-binding protein Replication Protein A (RPA). HARP has been implicated in maintaining genome integrity through its role in DNA replication and repair, two processes that generate RPA-coated ssDNA. In addition, mutations in HARP cause a rare disease known as Schimke immuno-osseous dysplasia. In this study, we purified HARP containing complexes with the goal of identifying the predominant factors that stably associate with HARP. We found that HARP preferentially interacts with RPA molecules that are bound to the DNA-dependent protein kinase (DNA-PK). We also found that RPA is phosphorylated by DNA-PK in vitro, while the RPA-HARP complexes are not. Our results suggest that, in addition to its annealing helicase activity, which eliminates the natural binding substrate for RPA, HARP blocks the phosphorylation of RPA by DNA-PK.

  14. Force regulated dynamics of RPA on a DNA fork.

    Science.gov (United States)

    Kemmerich, Felix E; Daldrop, Peter; Pinto, Cosimo; Levikova, Maryna; Cejka, Petr; Seidel, Ralf

    2016-07-08

    Replication protein A (RPA) is a single-stranded DNA binding protein, involved in most aspects of eukaryotic DNA metabolism. Here, we study the behavior of RPA on a DNA substrate that mimics a replication fork. Using magnetic tweezers we show that both yeast and human RPA can open forked DNA when sufficient external tension is applied. In contrast, at low force, RPA becomes rapidly displaced by the rehybridization of the DNA fork. This process appears to be governed by the binding or the release of an RPA microdomain (toehold) of only few base-pairs length. This gives rise to an extremely rapid exchange dynamics of RPA at the fork. Fork rezipping rates reach up to hundreds of base-pairs per second, being orders of magnitude faster than RPA dissociation from ssDNA alone. Additionally, we show that RPA undergoes diffusive motion on ssDNA, such that it can be pushed over long distances by a rezipping fork. Generally the behavior of both human and yeast RPA homologs is very similar. However, in contrast to yeast RPA, the dissociation of human RPA from ssDNA is greatly reduced at low Mg(2+) concentrations, such that human RPA can melt DNA in absence of force. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. The 1993 RPA timber assessment update

    Science.gov (United States)

    Richard W. Haynes; Darius M. Adams; John R. Mills

    1995-01-01

    This update reports changes in the Nation's timber resource since the 1989 RPA timber assessment. The timber resource situation is analyzed to provide projections for future cost and availability of timber products to meet demands. Prospective trends in demands for and supplies of timber, and the factors that affect these trends are examined. These include changes...

  16. Second RPA dynamics at finite temperature: time-evolutions of dynamical operators

    International Nuclear Information System (INIS)

    Jang, S.

    1989-01-01

    Time-evolutions of dynamical operators, in particular the generalized density matrix comprising both diagonal and off-diagonal elements, are investigated within the framework of second RPA dynamics at finite temperature. The calculation of the density matrix previously carried out through the appliance of the second RPA master equation by retaining only the slowly oscillating coupling terms is extended to include in the interaction Hamiltonian both the rapidly and slowly oscillating coupling terms. The extended second RPA master equation, thereby formulated without making use of the so-called resonant approximation, is analytically solved and a closed expression for the generalized density matrix is extracted. We provide illustrative examples of the generalized density matrix for various specific initial conditions. We turn particularly our attention to the Poisson distribution type of initial condition for which we deduce specifically a particular form of the density matrix from the solution of the Fokker-Planck equation for the coherent state representation. The relation of the Fokker-Planck equation to the second RPA master equation and its properties are briefly discussed. The oversight incurred in the time-evolution of operators by the resonant approximation is elucidated. The first and second moments of collective coordinates are also computed in relation to the expectation value of various dynamical operators involved in the extended master equation

  17. Identification of proteins that may directly interact with human RPA.

    Science.gov (United States)

    Nakaya, Ryou; Takaya, Junichiro; Onuki, Takeshi; Moritani, Mariko; Nozaki, Naohito; Ishimi, Yukio

    2010-11-01

    RPA, which consisted of three subunits (RPA1, 2 and 3), plays essential roles in DNA transactions. At the DNA replication forks, RPA binds to single-stranded DNA region to stabilize the structure and to assemble other replication proteins. Interactions between RPA and several replication proteins have been reported but the analysis is not comprehensive. We systematically performed the qualitative analysis to identify RPA interaction partners to understand the protein-protein interaction at the replication forks. We expressed in insect cells the three subunits of human RPA, together with one replication protein, which is present at the forks under normal conditions and/or under the replication stress conditions, to examine the interaction. Among 30 proteins examined in total, it was found that at least 14 proteins interacted with RPA. RPA interacted with MCM3-7, MCM-BP and CDC45 proteins among the proteins that play roles in the initiation and the elongation of the DNA replication. RPA bound with TIPIN, CLASPIN and RAD17, which are involved in the DNA replication checkpoint functions. RPA also bound with cyclin-dependent kinases and an amino-terminal fragment of Rb protein that negatively regulates DNA replication. These results suggest that RPA interacts with the specific proteins among those that play roles in the regulation of the replication fork progression.

  18. Analysis list: Rpa1 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Rpa1 Blood,Embryonic fibroblast,Spleen + mm9 http://dbarchive.biosciencedbc.jp/kyus...hu-u/mm9/target/Rpa1.1.tsv http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/target/Rpa1.5.tsv http://dbarchive.bioscience...dbc.jp/kyushu-u/mm9/target/Rpa1.10.tsv http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/colo/Rpa1.B...lood.tsv,http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/colo/Rpa1.Embryonic_fibro...blast.tsv,http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/colo/Rpa1.Spleen.tsv http://dbarchive.biosciencedbc

  19. Functions of alternative Replication Protein A (aRPA) in initiation and elongation

    OpenAIRE

    Mason, Aaron C.; Roy, Rupa; Simmons, Daniel T.; Wold, Marc S.

    2010-01-01

    Replication protein A (RPA) is a single-stranded DNA-binding complex that is essential for DNA replication, repair and recombination in eukaryotic cells. In addition to this canonical complex, we have recently characterized an alternative Replication Protein A complex (aRPA) that is unique to primates. aRPA is composed of three subunits: RPA1 and RPA3, also present in canonical RPA, and a primate-specific subunit RPA4, homologous to canonical RPA2. aRPA has biochemical properties similar to t...

  20. Nonlinear diffuse scattering of the random-phased wave

    International Nuclear Information System (INIS)

    Kato, Yoshiaki; Arinaga, Shinji; Mima, Kunioki.

    1983-01-01

    First experimental observation of the nonlinear diffuse scattering is reported. This new effect was observed in the propagation of the random-phased wave through a nonlinear dielectric medium. This effect is ascribed to the diffusion of the wavevector of the electro-magnetic wave to the lateral direction due to the randomly distributed nonlinear increase in the refractive index. (author)

  1. Lyapunov stability and poisson structure of the thermal TDHF and RPA equations

    International Nuclear Information System (INIS)

    Balian, R.; Veneroni, M.

    1989-01-01

    The thermal TDHF equation is analyzed in the Liouville representation of quantum mechanics, where the matrix elements of the single-particle (s.p) density ρ behave as classical dynamical variables. By introducing the Lie--Poisson bracket associated with the unitary group of the s.p. Hilbert space, we show that TDHF has a Hamiltonian, but non-canonical, classical form. Within this Poisson structure, either the s.p. energy or the s.p. grand potential Ω(ρ) act as a Hamilton function. The Lyapunov stability of both the TDHF and RPA equations around a HF state then follows, since the HF approximation for thermal equilibrium is determined by minimizing Ω(ρ). The RPA matrix in the Liouville space is expressed as the product of the Poisson tensor with the HF stability matrix, interpreted as a metric tensor generated by the entropy. This factorization displays the roles of the energy and entropy terms arising from Ω(ρ) in the RPA dynamics, and it helps to construct the RPA modes. Several extensions are considered. copyright 1989 Academic Press, Inc

  2. Lyapunov stability and Poisson structure of the thermal TDHF and RPA equations

    International Nuclear Information System (INIS)

    Veneroni, M.; Balian, R.

    1989-01-01

    The thermal TDHF equation is analyzed in the Liouville representation of quantum mechanics, where the matrix elements of the single-particle (s.p.) density ρ behave as classical dynamical variables. By introducing the Lie-Poisson bracket associated with the unitary group of the s.p. Hilbert space, we show that TDHF has a hamiltonian, but non-canonical, classical form. Within this Poisson structure, either the s.p. energy or the s.p. grand potential Ω(ρ) act as a Hamilton function. The Lyapunov stability of both the TDHF and RPA equations around a HF state then follows, since the HF approximation for thermal equilibrium is determined by minimizing Ω(ρ). The RPA matrix in the Liouville space is expressed as the product of the Poisson tensor with the HF stability matrix, interpreted as a metric tensor generated by the entropy. This factorization displays the roles of the energy and entropy terms arising from Ω(ρ) in the RPA dynamics, and it helps to construct the RPA modes. Several extensions are considered

  3. Analysis of data from Viking RPA's

    Science.gov (United States)

    Hanson, W. B.

    1981-01-01

    Measurements of the martian ionosphere performed by Viking Retarding Potential Analyzer (RPA) are reported. Viking RPA measurements of low energy electron fluxes out to 16,000 km above the Mars surface are discussed including both energy spectra and periods of continuous monitoring of the total flux above 15 ev. The mean electron current at energies greater than ev increases montonically by nearly two orders of magnitude from about 9000 km down to 700 km, but no clear signature of the bow shock is seen. The total wave power in the 2 sec measurement intervals for this current does, however, show a broad peak near 1700 km altitude. These variations in the low energy electron fluxes are related to whistler mode oscillations in the solar wind plasma. It is concluded that there may be a highly turbulent shock structure that masks a clear signature of the bow shock in the time averaged data.

  4. Magnetocaloric effect (MCE): Microscopic approach within Tyablikov approximation for anisotropic ferromagnets

    Energy Technology Data Exchange (ETDEWEB)

    Kotelnikova, O.A.; Prudnikov, V.N. [Physical Faculty, Lomonosov State University, Department of Magnetism, Moscow (Russian Federation); Rudoy, Yu.G., E-mail: rudikar@mail.ru [People' s Friendship University of Russia, Department of Theoretical Physics, Moscow (Russian Federation)

    2015-06-01

    The aim of this paper is to generalize the microscopic approach to the description of the magnetocaloric effect (MCE) started by Kokorina and Medvedev (E.E. Kokorina, M.V. Medvedev, Physica B 416 (2013) 29.) by applying it to the anisotropic ferromagnet of the “easy axis” type in two settings—with external magnetic field parallel and perpendicular to the axis of easy magnetization. In the last case there appears the field induced (or spin-reorientation) phase transition which occurs at the critical value of the external magnetic field. This value is proportional to the exchange anisotropy constant at low temperatures, but with the rise of temperature it may be renormalized (as a rule, proportional to the magnetization). We use the explicit form of the Hamiltonian of the anisotropic ferromagnet and apply widely used random phase approximation (RPA) (known also as Tyablikov approximation in the Green function method) which is more accurate than the well known molecular field approximation (MFA). It is shown that in the first case the magnitude of MCE is raised whereas in the second one the MCE disappears due to compensation of the critical field renormalized with the magnetization.

  5. ATR Prohibits Replication Catastrophe by Preventing Global Exhaustion of RPA

    DEFF Research Database (Denmark)

    Toledo Lazaro, Luis Ignacio; Altmeyer, Matthias; Rask, Maj-Britt

    2013-01-01

    origin firing generates an excess of single-stranded DNA that exhausts the nuclear pool of RPA. Partial reduction of RPA accelerated fork breakage, and forced elevation of RPA was sufficient to delay such "replication catastrophe" even in the absence of ATR activity. Conversely, unscheduled origin firing...... induced breakage of stalled forks even in cells with active ATR. Thus, ATR-mediated suppression of dormant origins shields active forks against irreversible breakage via preventing exhaustion of nuclear RPA. This study elucidates how replicating genomes avoid destabilizing DNA damage. Because cancer cells...

  6. Lowest-order corrections to the RPA polarizability and GW self-energy of a semiconducting wire

    NARCIS (Netherlands)

    Groot, de H.J.; Ummels, R.T.M.; Bobbert, P.A.; van Haeringen, W.

    1996-01-01

    We present the results of the addition of lowest-order vertex and self-consistency corrections to the RPA polarizability and the GW self-energy for a semiconducting wire. It is found that, when starting from a local density approximation zeroth-order Green function and systematically including these

  7. Genetic analysis of RPA single-stranded DNA binding protein in Haloferax volcanii

    OpenAIRE

    Stroud, A. L.

    2012-01-01

    Replication protein A (RPA) is a single-stranded DNA-binding protein that is present in all three domains of life. The roles of RPA include stabilising and protecting single- stranded DNA from nuclease degradation during DNA replication and repair. To achieve this, RPA uses an oligosaccharide-binding fold (OB fold) to bind single- stranded DNA. Haloferax volcanii encodes three RPAs – RPA1, RPA2 and RPA3, of which rpa1 and rpa3 are in operons with genes encoding associated proteins (APs). ...

  8. RPA-1 from Leishmania amazonensis (LaRPA-1) structurally differs from other eukaryote RPA-1 and interacts with telomeric DNA via its N-terminal OB-fold domain.

    Science.gov (United States)

    Pavani, R S; Fernandes, C; Perez, A M; Vasconcelos, E J R; Siqueira-Neto, J L; Fontes, M R; Cano, M I N

    2014-12-20

    Replication protein A-1 (RPA-1) is a single-stranded DNA-binding protein involved in DNA metabolism. We previously demonstrated the interaction between LaRPA-1 and telomeric DNA. Here, we expressed and purified truncated mutants of LaRPA-1 and used circular dichroism measurements and molecular dynamics simulations to demonstrate that the tertiary structure of LaRPA-1 differs from human and yeast RPA-1. LaRPA-1 interacts with telomeric ssDNA via its N-terminal OB-fold domain, whereas RPA from higher eukaryotes show different binding modes to ssDNA. Our results show that LaRPA-1 is evolutionary distinct from other RPA-1 proteins and can potentially be used for targeting trypanosomatid telomeres. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  9. RPA Data Wiz users guide, version 1.0

    Science.gov (United States)

    Scott A. Pugh

    2004-01-01

    RPA Data Wiz is a computer application use to create summary tables, graphs, and maps of Resource Planning Act (RPA) Assessment forest information (English or metric units). Volumes for growing stock, live cull, dead salvable, netgrowth, and mortality can be estimated. Acreage, biomass, and tree count estimates are also available.

  10. The 2002 RPA Plot Summary database users manual

    Science.gov (United States)

    Patrick D. Miles; John S. Vissage; W. Brad Smith

    2004-01-01

    Describes the structure of the RPA 2002 Plot Summary database and provides information on generating estimates of forest statistics from these data. The RPA 2002 Plot Summary database provides a consistent framework for storing forest inventory data across all ownerships across the entire United States. The data represents the best available data as of October 2001....

  11. Calculation of the collective mass-parameter including RPA corrections

    International Nuclear Information System (INIS)

    Pal, M.K.; Zawischa, D.; Speth, J.

    1975-01-01

    A derivation of the vibrational mass-parameter B is given which makes the consistency with RPA calculations explicit. The expected enhancement by the residual particle-hole and particle-particle interaction is demonstrated by solving the quasiparticle-RPA for deformed nuclei in the rare earth region. (orig.) [de

  12. RpA ratio: total shadowing due to running coupling

    OpenAIRE

    Iancu, E.; Triantafyllopoulos, D. N.

    2007-01-01

    We predict that the RpA ratio at the most forward rapidities to be measured at LHC should be strongly suppressed, close to "total shadowing'' (RpA = A^(-1/3)), as a consequence of running coupling effects in the nonlinear QCD evolution.

  13. RPA Assessment of Outdoor Recreation: Past, Current, and Future Directions

    Science.gov (United States)

    John C. Bergstrom; H. Ken Cordell

    1994-01-01

    In this paper, the outdoor recreation sections of the Renewable Resource Planning Act (RPA) Assessments conducted to date are reviewed. Current policy and mangement applications of the outsdoor recreation results published in 1989 Assessment are discussed also. The paper concludes with suggestions for the assemssment of outdoor recreation in future RPA Assessements...

  14. Some applications of renormalized RPA in bosonic field theories

    International Nuclear Information System (INIS)

    Hansen, H.; Chanfray, G.

    2003-01-01

    We present some applications of the renormalized RPA in bosonic field theories. We first present some developments for the explicit calculation of the total energy in Φ 4 theory and discuss its phase structure in 1 + 1 dimensions. We also demonstrate that the Goldstone theorem is satisfied in the O(N) model within the renormalized RPA. (authors)

  15. 76 FR 54195 - 2010 Resources Planning Act (RPA) Assessment Draft

    Science.gov (United States)

    2011-08-31

    ... Resources Planning Act (RPA) Assessment is available for review and comment at http://www.fs.fed.us/research... facsimile to 703-605-5131 or by email using the comment form on the Web site http://www.fs.fed.us/research... . Additional information about the RPA Assessment can be obtained on the Internet at http://www.fs.fed.us...

  16. RPA physically interacts with the human DNA glycosylase NEIL1 to regulate excision of oxidative DNA base damage in primer-template structures.

    Science.gov (United States)

    Theriot, Corey A; Hegde, Muralidhar L; Hazra, Tapas K; Mitra, Sankar

    2010-06-04

    The human DNA glycosylase NEIL1, activated during the S-phase, has been shown to excise oxidized base lesions in single-strand DNA substrates. Furthermore, our previous work demonstrating functional interaction of NEIL1 with PCNA and flap endonuclease 1 (FEN1) suggested its involvement in replication-associated repair. Here we show interaction of NEIL1 with replication protein A (RPA), the heterotrimeric single-strand DNA binding protein that is essential for replication and other DNA transactions. The NEIL1 immunocomplex isolated from human cells contains RPA, and its abundance in the complex increases after exposure to oxidative stress. NEIL1 directly interacts with the large subunit of RPA (K(d) approximately 20 nM) via the common interacting interface (residues 312-349) in NEIL1's disordered C-terminal region. RPA inhibits the base excision activity of both wild-type NEIL1 (389 residues) and its C-terminal deletion CDelta78 mutant (lacking the interaction domain) for repairing 5-hydroxyuracil (5-OHU) in a primer-template structure mimicking the DNA replication fork. This inhibition is reduced when the damage is located near the primer-template junction. Contrarily, RPA moderately stimulates wild-type NEIL1 but not the CDelta78 mutant when 5-OHU is located within the duplex region. While NEIL1 is inhibited by both RPA and Escherichia coli single-strand DNA binding protein, only inhibition by RPA is relieved by PCNA. These results showing modulation of NEIL1's activity on single-stranded DNA substrate by RPA and PCNA support NEIL1's involvement in repairing the replicating genome. Copyright 2010 Elsevier B.V. All rights reserved.

  17. RPA homologs and ssDNA processing during meiotic recombination.

    Science.gov (United States)

    Ribeiro, Jonathan; Abby, Emilie; Livera, Gabriel; Martini, Emmanuelle

    2016-06-01

    Meiotic homologous recombination is a specialized process that involves homologous chromosome pairing and strand exchange to guarantee proper chromosome segregation and genetic diversity. The formation and repair of DNA double-strand breaks (DSBs) during meiotic recombination differs from those during mitotic recombination in that the homologous chromosome rather than the sister chromatid is the preferred repair template. The processing of single-stranded DNA (ssDNA) formed on intermediate recombination structures is central to driving the specific outcomes of DSB repair during meiosis. Replication protein A (RPA) is the main ssDNA-binding protein complex involved in DNA metabolism. However, the existence of RPA orthologs in plants and the recent discovery of meiosis specific with OB domains (MEIOB), a widely conserved meiosis-specific RPA1 paralog, strongly suggest that multiple RPA complexes evolved and specialized to subdivide their roles during DNA metabolism. Here we review ssDNA formation and maturation during mitotic and meiotic recombination underlying the meiotic specific features. We describe and discuss the existence and properties of MEIOB and multiple RPA subunits in plants and highlight how they can provide meiosis-specific fates to ssDNA processing during homologous recombination. Understanding the functions of these RPA homologs and how they interact with the canonical RPA subunits is of major interest in the fields of meiosis and DNA repair.

  18. RPA and POT1: friends or foes at telomeres?

    Science.gov (United States)

    Flynn, Rachel Litman; Chang, Sandy; Zou, Lee

    2012-02-15

    Telomere maintenance in cycling cells relies on both DNA replication and capping by the protein complex shelterin. Two single-stranded DNA (ssDNA)-binding proteins, replication protein A (RPA) and protection of telomere 1 (POT1) play critical roles in DNA replication and telomere capping, respectively. While RPA binds to ssDNA in a non-sequence-specific manner, POT1 specifically recognizes singlestranded TTAGGG telomeric repeats. Loss of POT1 leads to aberrant accumulation of RPA at telomeres and activation of the ataxia telangiectasia and Rad3-related kinase (ATR)-mediated checkpoint response, suggesting that POT1 antagonizes RPA binding to telomeric ssDNA. The requirement for both POT1 and RPA in telomere maintenance and the antagonism between the two proteins raises the important question of how they function in concert on telomeric ssDNA. Two interesting models were proposed by recent studies to explain the regulation of POT1 and RPA at telomeres. Here, we discuss how these models help unravel the coordination, and also the antagonism, between POT1 and RPA during the cell cycle.

  19. Extended RPA study of nuclear collective phenomena

    International Nuclear Information System (INIS)

    Drozdz, S.

    1987-01-01

    A fully microscopic study of nuclear collective phenomena is presented within the framework of an extended RPA which includes 1p-1h and 2p-2h excitations in a consistent way. This theory allows us to obtain a very realistic description of various excitation spectra. As a result, a strong evidence of correlation effects beyond mean-field theory emerges. The effective interaction used is a G-matrix derived from the meson-exchange potential. The extended theory introduces also additional correlations which screen the long-large part of the effective interaction. This effect significantly enhances the stability of the ground state against density fluctuations. In this connection a possible importance of relativistic effects is also discussed. 99 refs., 19 figs., 5 tabs. (author)

  20. Key-space analysis of double random phase encryption technique

    Science.gov (United States)

    Monaghan, David S.; Gopinathan, Unnikrishnan; Naughton, Thomas J.; Sheridan, John T.

    2007-09-01

    We perform a numerical analysis on the double random phase encryption/decryption technique. The key-space of an encryption technique is the set of possible keys that can be used to encode data using that technique. In the case of a strong encryption scheme, many keys must be tried in any brute-force attack on that technique. Traditionally, designers of optical image encryption systems demonstrate only how a small number of arbitrary keys cannot decrypt a chosen encrypted image in their system. However, this type of demonstration does not discuss the properties of the key-space nor refute the feasibility of an efficient brute-force attack. To clarify these issues we present a key-space analysis of the technique. For a range of problem instances we plot the distribution of decryption errors in the key-space indicating the lack of feasibility of a simple brute-force attack.

  1. ATR prohibits replication catastrophe by preventing global exhaustion of RPA.

    Science.gov (United States)

    Toledo, Luis Ignacio; Altmeyer, Matthias; Rask, Maj-Britt; Lukas, Claudia; Larsen, Dorthe Helena; Povlsen, Lou Klitgaard; Bekker-Jensen, Simon; Mailand, Niels; Bartek, Jiri; Lukas, Jiri

    2013-11-21

    ATR, activated by replication stress, protects replication forks locally and suppresses origin firing globally. Here, we show that these functions of ATR are mechanistically coupled. Although initially stable, stalled forks in ATR-deficient cells undergo nucleus-wide breakage after unscheduled origin firing generates an excess of single-stranded DNA that exhausts the nuclear pool of RPA. Partial reduction of RPA accelerated fork breakage, and forced elevation of RPA was sufficient to delay such "replication catastrophe" even in the absence of ATR activity. Conversely, unscheduled origin firing induced breakage of stalled forks even in cells with active ATR. Thus, ATR-mediated suppression of dormant origins shields active forks against irreversible breakage via preventing exhaustion of nuclear RPA. This study elucidates how replicating genomes avoid destabilizing DNA damage. Because cancer cells commonly feature intrinsically high replication stress, this study also provides a molecular rationale for their hypersensitivity to ATR inhibitors. Copyright © 2013 Elsevier Inc. All rights reserved.

  2. AF RPA Training: Utility and Tradition in Conflict

    Science.gov (United States)

    2017-06-01

    and children. My wife’s patience, understanding, and sacrifice permitted me to focus on the academic material and writing , neither of which came...for a training strategy that leverages the RPA weapon system’s unique modularity to produce well-trained RPA pilots more quickly. vii...momentum. He states, “The social constructivists have a key to understanding the behavior of young systems; technical

  3. BLM and RMI1 alleviate RPA inhibition of TopoIIIα decatenase activity.

    Science.gov (United States)

    Yang, Jay; Bachrati, Csanad Z; Hickson, Ian D; Brown, Grant W

    2012-01-01

    RPA is a single-stranded DNA binding protein that physically associates with the BLM complex. RPA stimulates BLM helicase activity as well as the double Holliday junction dissolution activity of the BLM-topoisomerase IIIα complex. We investigated the effect of RPA on the ssDNA decatenase activity of topoisomerase IIIα. We found that RPA and other ssDNA binding proteins inhibit decatenation by topoisomerase IIIα. Complex formation between BLM, TopoIIIα, and RMI1 ablates inhibition of decatenation by ssDNA binding proteins. Together, these data indicate that inhibition by RPA does not involve species-specific interactions between RPA and BLM-TopoIIIα-RMI1, which contrasts with RPA modulation of double Holliday junction dissolution. We propose that topoisomerase IIIα and RPA compete to bind to single-stranded regions of catenanes. Interactions with BLM and RMI1 enhance toposiomerase IIIα activity, promoting decatenation in the presence of RPA.

  4. Laser-beam apodization with a graded random phase window

    Energy Technology Data Exchange (ETDEWEB)

    Haas, R.A.; Summers, M.A.; Linford, G.J.

    1986-10-01

    Experiments and analysis indicate that graded random phase modulation can be usesd to apodize a laser beam. In the case of an obscuration or a hard edge it can prevent the formation of Fresnel-diffraction ripples. For example, here the interaction of a 1-..mu..m-wavelength laser beam with a central obscuration of half-width a -- 100 ..mu..m is studied theoretically. It is found that if the exit surface of a window, placed immediately downstream of the obstacle, is randomly modulated with a Gaussian amplitude transverse correlation length l -- 50..mu..m and a mean-square amplitude that decreases exponentially from a peak height of --1..mu..m/sup 2/ away from the center of the obscuration with transverse scale length L -- 500 ..mu..m, then the Fresenel-diffraction ripples normally produced by the obscuration are elimated. The scaling of these results is also discussed. The calculations are in general agreement with experimental results.

  5. Laser-beam apodization with a graded random phase window

    International Nuclear Information System (INIS)

    Haas, R.A.; Summers, M.A.; Linford, G.J.

    1986-01-01

    Experiments and analysis indicate that graded random phase modulation can be usesd to apodize a laser beam. In the case of an obscuration or a hard edge it can prevent the formation of Fresnel-diffraction ripples. For example, here the interaction of a 1-μm-wavelength laser beam with a central obscuration of half-width a -- 100 μm is studied theoretically. It is found that if the exit surface of a window, placed immediately downstream of the obstacle, is randomly modulated with a Gaussian amplitude transverse correlation length l -- 50μm and a mean-square amplitude that decreases exponentially from a peak height of --1μm 2 away from the center of the obscuration with transverse scale length L -- 500 μm, then the Fresenel-diffraction ripples normally produced by the obscuration are elimated. The scaling of these results is also discussed. The calculations are in general agreement with experimental results

  6. Physical and functional interactions of Caenorhabditis elegans WRN-1 helicase with RPA-1.

    Science.gov (United States)

    Hyun, Moonjung; Park, Sojin; Kim, Eunsun; Kim, Do-Hyung; Lee, Se-Jin; Koo, Hyeon-Sook; Seo, Yeon-Soo; Ahn, Byungchan

    2012-02-21

    The Caenorhabditis elegans Werner syndrome protein, WRN-1, a member of the RecQ helicase family, has a 3'-5' DNA helicase activity. Worms with defective wrn-1 exhibit premature aging phenotypes and an increased level of genome instability. In response to DNA damage, WRN-1 participates in the initial stages of checkpoint activation in concert with C. elegans replication protein A (RPA-1). WRN-1 helicase is stimulated by RPA-1 on long DNA duplex substrates. However, the mechanism by which RPA-1 stimulates DNA unwinding and the function of the WRN-1-RPA-1 interaction are not clearly understood. We have found that WRN-1 physically interacts with two RPA-1 subunits, CeRPA73 and CeRPA32; however, full-length WRN-1 helicase activity is stimulated by only the CeRPA73 subunit, while the WRN-1(162-1056) fragment that harbors the helicase activity requires both the CeRPA73 and CeRPA32 subunits for the stimulation. We also found that the CeRPA73(1-464) fragment can stimulate WRN-1 helicase activity and that residues 335-464 of CeRPA73 are important for physical interaction with WRN-1. Because CeRPA73 and the CeRPA73(1-464) fragment are able to bind single-stranded DNA (ssDNA), the stimulation of WRN-1 helicase by RPA-1 is most likely due to the ssDNA binding activity of CeRPA73 and the direct interaction of WRN-1 and CeRPA73.

  7. Human PrimPol activity is enhanced by RPA.

    Science.gov (United States)

    Martínez-Jiménez, María I; Lahera, Antonio; Blanco, Luis

    2017-04-10

    Human PrimPol is a primase belonging to the AEP superfamily with the unique ability to synthesize DNA primers de novo, and a non-processive DNA polymerase able to bypass certain DNA lesions. PrimPol facilitates both mitochondrial and nuclear replication fork progression either acting as a conventional TLS polymerase, or repriming downstream of blocking lesions. In vivo assays have shown that PrimPol is rapidly recruited to sites of DNA damage by interaction with the human replication protein A (RPA). In agreement with previous findings, we show here that the higher affinity of RPA for ssDNA inhibits PrimPol activities in short ssDNA templates. In contrast, once the amount of ssDNA increases up to a length in which both proteins can simultaneously bind ssDNA, as expected during replicative stress conditions, PrimPol and RPA functionally interact, and their binding capacities are mutually enhanced. When using M13 ssDNA as template, RPA stimulated both the primase and polymerase activities of PrimPol, either alone or in synergy with Polε. These new findings supports the existence of a functional PrimPol/RPA association that allows repriming at the exposed ssDNA regions formed in the leading strand upon replicase stalling.

  8. Mechanochemical regulations of RPA's binding to ssDNA

    Science.gov (United States)

    Chen, Jin; Le, Shimin; Basu, Anindita; Chazin, Walter J.; Yan, Jie

    2015-03-01

    Replication protein A (RPA) is a ubiquitous eukaryotic single-stranded DNA (ssDNA) binding protein that serves to protect ssDNA from degradation and annealing, and as a template for recruitment of many downstream factors in virtually all DNA transactions in cell. During many of these transactions, DNA is tethered and is likely subject to force. Previous studies of RPA's binding behavior on ssDNA were conducted in the absence of force; therefore the RPA-ssDNA conformations regulated by force remain unclear. Here, using a combination of atomic force microscopy imaging and mechanical manipulation of single ssDNA tethers, we show that force mediates a switch of the RPA bound ssDNA from amorphous aggregation to a much more regular extended conformation. Further, we found an interesting non-monotonic dependence of the binding affinity on monovalent salt concentration in the presence of force. In addition, we discovered that zinc in micromolar concentrations drives ssDNA to a unique, highly stiff and more compact state. These results provide new mechanochemical insights into the influences and the mechanisms of action of RPA on large single ssDNA.

  9. BLM and RMI1 Alleviate RPA Inhibition of TopoIIIa Decatenase Activity

    DEFF Research Database (Denmark)

    Yang, Jay; Bachrati, Csanad Z; Hickson, Ian D

    2012-01-01

    RPA is a single-stranded DNA binding protein that physically associates with the BLM complex. RPA stimulates BLM helicase activity as well as the double Holliday junction dissolution activity of the BLM-topoisomerase IIIa complex. We investigated the effect of RPA on the ssDNA decatenase activity...... of topoisomerase IIIa. We found that RPA and other ssDNA binding proteins inhibit decatenation by topoisomerase IIIa. Complex formation between BLM, TopoIIIa, and RMI1 ablates inhibition of decatenation by ssDNA binding proteins. Together, these data indicate that inhibition by RPA does not involve species......-specific interactions between RPA and BLM-TopoIIIa-RMI1, which contrasts with RPA modulation of double Holliday junction dissolution. We propose that topoisomerase IIIa and RPA compete to bind to single-stranded regions of catenanes. Interactions with BLM and RMI1 enhance toposiomerase IIIa activity, promoting...

  10. A method for the solution of the RPA eigenvalue

    International Nuclear Information System (INIS)

    Hoffman, M.J.H.; De Kock, P.R.

    1986-01-01

    The RPA eigenvalue problem requires the diagonalization of a 2nx2n matrix. In practical calculations, n (the number of particle-hole basis states) can be a few hundred and the diagonalization of such a large non-symmetric matrix may take quite a long time. In this report we firstly discuss sufficient conditions for real and non-zero RPA eigenvalues. The presence of zero or imaginary eigenvalues is related to the relative importance of the groundstate correlations to the total interaction energy. We then rewrite the RPA eigenvalue problem for the cases where these conditions are fulfilled in a form which only requires the diagonalization of two symmetric nxn matrices. The extend to which this method can be applied when zero eigenvalues occur, is also discussed

  11. Combination of Wavefunction and Density Functional Approximations for Describing Electronic Correlation

    Science.gov (United States)

    Garza, Alejandro J.

    history in quantum chemistry (practical implementations have appeared in the literature since the 1970s). However, this kind of techniques have not achieved widespread use due to problems such as double counting of correlation and the symmetry dilemma--the fact that wavefunction methods respect the symmetries of Hamiltonian, while modern functionals are designed to work with broken symmetry densities. Here, particular mathematical features of pCCD and CCD0 are exploited to avoid these problems in an efficient manner. The two resulting families of approximations, denoted as pCCD+DFT and CCD0+DFT, are shown to be able to describe static and dynamic correlation in standard benchmark calculations. Furthermore, it is also shown that CCD0+DFT lends itself to combination with correlation from the direct random phase approximation (dRPA). Inclusion of dRPA in the long-range via the technique of range-separation allows for the description of dispersion correlation, the remaining part of the correlation. Thus, when combined with the dRPA, CCD0+DFT can account for all three-types of electron correlation that are necessary to accurately describe molecular systems. Lastly, applications of CCD0+DFT to actinide chemistry are considered in this work. The accuracy of CCD0+DFT for predicting equilibrium geometries and vibrational frequencies of actinide molecules and ions is assessed and compared to that of well-established quantum chemical methods. For this purpose, the f0 actinyl series (UO2 2+, NpO 23+, PuO24+, the isoelectronic NUN, and Thorium (ThO, ThO2+) and Nobelium (NoO, NoO2) oxides are studied. It is shown that the CCD0+DFT description of these species agrees with available experimental data and is comparable with the results given by the highest-level calculations that are possible for such heavy compounds while being, at least, an order of magnitude lower in computational cost.

  12. Binding polarity of RPA to telomeric sequences and influence of G-quadruplex stability.

    Science.gov (United States)

    Safa, Layal; Delagoutte, Emmanuelle; Petruseva, Irina; Alberti, Patrizia; Lavrik, Olga; Riou, Jean-François; Saintomé, Carole

    2014-08-01

    Replication protein A (RPA) is a single-stranded DNA binding protein that plays an essential role in telomere maintenance. RPA binds to and unfolds G-quadruplex (G4) structures formed in telomeric DNA, thus facilitating lagging strand DNA replication and telomerase activity. To investigate the effect of G4 stability on the interactions with human RPA (hRPA), we used a combination of biochemical and biophysical approaches. Our data revealed an inverse relationship between G4 stability and ability of hRPA to bind to telomeric DNA; notably small G4 ligands that enhance G4 stability strongly impaired G4 unfolding by hRPA. To gain more insight into the mechanism of binding and unfolding of telomeric G4 structures by RPA, we carried out photo-crosslinking experiments to elucidate the spatial arrangement of the RPA subunits along the DNA strands. Our results showed that RPA1 and RPA2 are arranged from 5' to 3' along the unfolded telomeric G4, as already described for unstructured single-stranded DNA, while no contact is possible with RPA3 on this short oligonucleotide. In addition, these data are compatible with a 5' to 3' directionality in G4 unfolding by hRPA. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  13. Future scenarios: a technical document supporting the Forest Service 2010 RPA Assessment

    Science.gov (United States)

    . USDA Forest Service.

    2012-01-01

    The Forest and Rangeland Renewable Resources Planning Act of 1974 (RPA) mandates a periodic assessment of the conditions and trends of the Nation's renewable resources on forests and rangelands. The RPA Assessment includes projections of resource conditions and trends 50 years into the future. The 2010 RPA Assessment used a set of future scenarios to provide a...

  14. Linking global scenarios to national assessments: Experiences from the Resources Planning Act (RPA) Assessment

    Science.gov (United States)

    Linda L. Langner; Peter J. Ince

    2012-01-01

    The Resources Planning Act (RPA) Assessment provides a nationally consistent analysis of the status and trends of the Nation's renewable forest resources. A global scenario approach was taken for the 2010 RPA Assessment to provide a shared world view of potential futures. The RPA Assessment scenarios were linked to the global scenarios and climate projections used...

  15. Self-consistent RPA based on a many-body vacuum

    International Nuclear Information System (INIS)

    Jemaï, M.; Schuck, P.

    2011-01-01

    Self-Consistent RPA is extended in a way so that it is compatible with a variational ansatz for the ground-state wave function as a fermionic many-body vacuum. Employing the usual equation-of-motion technique, we arrive at extended RPA equations of the Self-Consistent RPA structure. In principle the Pauli principle is, therefore, fully respected. However, the correlation functions entering the RPA matrix can only be obtained from a systematic expansion in powers of some combinations of RPA amplitudes. We demonstrate for a model case that this expansion may converge rapidly.

  16. Southern Forest Resource Assessment and Linkages to the National RPA

    Science.gov (United States)

    Fredrick Cubbage; Jacek Siry; Steverson Moffat; David N. Wear; Robert Abt

    1998-01-01

    We developed a Southern Forest Resource Assessment Consortium (SOFAC) in 1994, which is designed to enhance our capabilities to analyze and model the southern forest and timber resources. Southern growth and yield analyses prepared for the RPA via SOFAC indicate that substantial increases in timber productivity can occur given current technology. A survey about NIPF...

  17. Projecting national forest inventories for the 2000 RPA timber assessment.

    Science.gov (United States)

    John R. Mills; Xiaoping. Zhou

    2003-01-01

    National forest inventories were projected in a study that was part of the 2000 USDA Forest Service Resource Planning Act (RPA) timber assessment. This paper includes an overview of the status and structure of timber inventory of the National Forest System and presents 50-year projections under several scenarios. To examine a range of possible outcomes, results are...

  18. Grounding the RPA Force: Why Machine Needs Man

    Science.gov (United States)

    2016-06-01

    AU/ACSC/2016 AIR COMMAND AND STAFF COLLEGE AIR UNIVERSITY GROUNDING THE RPA FORCE: WHY MACHINE NEEDS MAN by Charles M. Washuk, Major, USAF (MBA...6 CHALLENGES OF MANNED FLIGHT...tactics will still require the presence of an operator, or “ man .” This paper focuses on the need for the Air Force to address the 18X career field and

  19. Enhancing Security of Double Random Phase Encoding Based on Random S-Box

    Science.gov (United States)

    Girija, R.; Singh, Hukum

    2018-06-01

    In this paper, we propose a novel asymmetric cryptosystem for double random phase encoding (DRPE) using random S-Box. While utilising S-Box separately is not reliable and DRPE does not support non-linearity, so, our system unites the effectiveness of S-Box with an asymmetric system of DRPE (through Fourier transform). The uniqueness of proposed cryptosystem lies on employing high sensitivity dynamic S-Box for our DRPE system. The randomness and scalability achieved due to applied technique is an additional feature of the proposed solution. The firmness of random S-Box is investigated in terms of performance parameters such as non-linearity, strict avalanche criterion, bit independence criterion, linear and differential approximation probabilities etc. S-Boxes convey nonlinearity to cryptosystems which is a significant parameter and very essential for DRPE. The strength of proposed cryptosystem has been analysed using various parameters such as MSE, PSNR, correlation coefficient analysis, noise analysis, SVD analysis, etc. Experimental results are conferred in detail to exhibit proposed cryptosystem is highly secure.

  20. Multi-kW coherent combining of fiber lasers seeded with pseudo random phase modulated light

    Science.gov (United States)

    Flores, Angel; Ehrehreich, Thomas; Holten, Roger; Anderson, Brian; Dajani, Iyad

    2016-03-01

    We report efficient coherent beam combining of five kilowatt-class fiber amplifiers with a diffractive optical element (DOE). Based on a master oscillator power amplifier (MOPA) configuration, the amplifiers were seeded with pseudo random phase modulated light. Each non-polarization maintaining fiber amplifier was optically path length matched and provides approximately 1.2 kW of near diffraction-limited output power (measured M2polarization control. A low power sample of the combined beam after the DOE provided an error signal for active phase locking which was performed via Locking of Optical Coherence by Single-Detector Electronic-Frequency Tagging (LOCSET). After phase stabilization, the beams were coherently combined via the 1x5 DOE. A total combined output power of 4.9 kW was achieved with 82% combining efficiency and excellent beam quality (M2splitter loss was 5%. Similarly, losses due in part to non-ideal polarization, ASE content, uncorrelated wavefront errors, and misalignment errors contributed to the efficiency reduction.

  1. Architecture and ssDNA interaction of the Timeless-Tipin-RPA complex.

    Science.gov (United States)

    Witosch, Justine; Wolf, Eva; Mizuno, Naoko

    2014-11-10

    The Timeless-Tipin (Tim-Tipin) complex, also referred to as the fork protection complex, is involved in coordination of DNA replication. Tim-Tipin is suggested to be recruited to replication forks via Replication Protein A (RPA) but details of the interaction are unknown. Here, using cryo-EM and biochemical methods, we characterized complex formation of Tim-Tipin, RPA and single-stranded DNA (ssDNA). Tim-Tipin and RPA form a 258 kDa complex with a 1:1:1 stoichiometry. The cryo-EM 3D reconstruction revealed a globular architecture of the Tim-Tipin-RPA complex with a ring-like and a U-shaped domain covered by a RPA lid. Interestingly, RPA in the complex adopts a horse shoe-like shape resembling its conformation in the presence of long ssDNA (>30 nucleotides). Furthermore, the recruitment of the Tim-Tipin-RPA complex to ssDNA is modulated by the RPA conformation and requires RPA to be in the more compact 30 nt ssDNA binding mode. The dynamic formation and disruption of the Tim-Tipin-RPA-ssDNA complex implicates the RPA-based recruitment of Tim-Tipin to the replication fork. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  2. Smoothing by spectral dispersion using random phase modulation for inertial confinement fusion

    International Nuclear Information System (INIS)

    Rothenberg, J.E.

    1995-01-01

    Numerical simulations of beam smoothing using random phase modulation and grating dispersion are presented. Spatial spectra of the target illumination show that significantly improved smoothing at low spatial frequency is achieved while maintaining uniform intensity in the laser amplifier

  3. Testing different brain metastasis grading systems in stereotactic radiosurgery: Radiation Therapy Oncology Group's RPA, SIR, BSBM, GPA, and modified RPA.

    Science.gov (United States)

    Serizawa, Toru; Higuchi, Yoshinori; Nagano, Osamu; Hirai, Tatsuo; Ono, Junichi; Saeki, Naokatsu; Miyakawa, Akifumi

    2012-12-01

    The authors conducted validity testing of the 5 major reported indices for radiosurgically treated brain metastases- the original Radiation Therapy Oncology Group's Recursive Partitioning Analysis (RPA), the Score Index for Radiosurgery in Brain Metastases (SIR), the Basic Score for Brain Metastases (BSBM), the Graded Prognostic Assessment (GPA), and the subclassification of RPA Class II proposed by Yamamoto-in nearly 2500 cases treated with Gamma Knife surgery (GKS), focusing on the preservation of neurological function as well as the traditional endpoint of overall survival. The authors analyzed data from 2445 cases treated with GKS by the first author (T.S.), the primary surgeon. The patient group consisted of 1716 patients treated between January 1998 and March 2008 (the Chiba series) and 729 patients treated between April 2008 and December 2011 (the Tokyo series). The interval from the date of GKS until the date of the patient's death (overall survival) and impaired activities of daily living (qualitative survival) were calculated using the Kaplan-Meier method, while the absolute risk for two adjacent classes of each grading system and both hazard ratios and 95% confidence intervals were estimated using the Cox proportional hazards model. For overall survival, there were highly statistically significant differences between each two adjacent patient groups characterized by class or score (all p values RPA appeared to be better than the original RPA and GPA. The modified RPA subclassification, proposed by Yamamoto, is well balanced in scoring simplicity with respect to case number distribution and statistical results for overall survival. However, a new or revised grading system is necessary for predicting qualitative survival and for selecting the optimal treatment for patients with brain metastasis treated by GKS.

  4. Skyrme RPA description of γ-vibrational states in rare-earth nuclei

    Directory of Open Access Journals (Sweden)

    Nesterenko V.O.

    2016-01-01

    Full Text Available The lowest γ-vibrational states with Kπ = 2+γ in well-deformed Dy, Er and Yb isotopes are investigated within the self-consistent separable quasiparticle random-phase-approximation (QRPA approach based on the Skyrme functional. The energies Eγ and reduced transition probabilities B(E2γ of the states are calculated with the Skyrme force SV-mas10. We demonstrate the strong effect of the pairing blocking on the energies of γ-vibrational states. It is also shown that collectivity of γ-vibrational states is strictly determined by keeping the Nilsson selection rules in the corresponding lowest 2qp configurations.

  5. Phosphorylated RPA recruits PALB2 to stalled DNA replication forks to facilitate fork recovery.

    Science.gov (United States)

    Murphy, Anar K; Fitzgerald, Michael; Ro, Teresa; Kim, Jee Hyun; Rabinowitsch, Ariana I; Chowdhury, Dipanjan; Schildkraut, Carl L; Borowiec, James A

    2014-08-18

    Phosphorylation of replication protein A (RPA) by Cdk2 and the checkpoint kinase ATR (ATM and Rad3 related) during replication fork stalling stabilizes the replisome, but how these modifications safeguard the fork is not understood. To address this question, we used single-molecule fiber analysis in cells expressing a phosphorylation-defective RPA2 subunit or lacking phosphatase activity toward RPA2. Deregulation of RPA phosphorylation reduced synthesis at forks both during replication stress and recovery from stress. The ability of phosphorylated RPA to stimulate fork recovery is mediated through the PALB2 tumor suppressor protein. RPA phosphorylation increased localization of PALB2 and BRCA2 to RPA-bound nuclear foci in cells experiencing replication stress. Phosphorylated RPA also stimulated recruitment of PALB2 to single-strand deoxyribonucleic acid (DNA) in a cell-free system. Expression of mutant RPA2 or loss of PALB2 expression led to significant DNA damage after replication stress, a defect accentuated by poly-ADP (adenosine diphosphate) ribose polymerase inhibitors. These data demonstrate that phosphorylated RPA recruits repair factors to stalled forks, thereby enhancing fork integrity during replication stress. © 2014 Murphy et al.

  6. Cdc45-induced loading of human RPA onto single-stranded DNA.

    Science.gov (United States)

    Szambowska, Anna; Tessmer, Ingrid; Prus, Piotr; Schlott, Bernhard; Pospiech, Helmut; Grosse, Frank

    2017-04-07

    Cell division cycle protein 45 (Cdc45) is an essential component of the eukaryotic replicative DNA helicase. We found that human Cdc45 forms a complex with the single-stranded DNA (ssDNA) binding protein RPA. Moreover, it actively loads RPA onto nascent ssDNA. Pull-down assays and surface plasmon resonance studies revealed that Cdc45-bound RPA complexed with ssDNA in the 8-10 nucleotide binding mode, but dissociated when RPA covered a 30-mer. Real-time analysis of RPA-ssDNA binding demonstrated that Cdc45 catalytically loaded RPA onto ssDNA. This placement reaction required physical contacts of Cdc45 with the RPA70A subdomain. Our results imply that Cdc45 controlled stabilization of the 8-nt RPA binding mode, the subsequent RPA transition into 30-mer mode and facilitated an ordered binding to ssDNA. We propose that a Cdc45-mediated loading guarantees a seamless deposition of RPA on newly emerging ssDNA at the nascent replication fork. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. Replication protein A, the laxative that keeps DNA regular: The importance of RPA phosphorylation in maintaining genome stability.

    Science.gov (United States)

    Byrne, Brendan M; Oakley, Gregory G

    2018-04-20

    The eukaryotic ssDNA-binding protein, Replication protein A (RPA), was first discovered almost three decades ago. Since then, much progress has been made to elucidate the critical roles for RPA in DNA metabolic pathways that help promote genomic stability. The canonical RPA heterotrimer (RPA1-3) is an essential coordinator of DNA metabolism that interacts with ssDNA and numerous protein partners to coordinate its roles in DNA replication, repair, recombination and telomere maintenance. An alternative form of RPA, termed aRPA, is formed by a complex of RPA4 with RPA1 and RPA3. aRPA is expressed differentially in cells compared to canonical RPA and has been shown to inhibit canonical RPA function while allowing for regular maintenance of cell viability. Interestingly, while aRPA is defective in DNA replication and cell cycle progression, it was shown to play a supporting role in nucleotide excision repair and recombination. The binding domains of canonical RPA interact with a growing number of partners involved in numerous genome maintenance processes. The protein interactions of the RPA-ssDNA complex are not only governed by competition between the binding proteins but also by post-translation modifications such as phosphorylation. Phosphorylation of RPA2 is an important post-translational modification of the RPA complex, and is essential for directing context-specific functions of the RPA complex in the DNA damage response. Due to the importance of RPA in cellular metabolism, it was identified as an appealing target for chemotherapeutic drug development that could be used in future cancer treatment regimens. Copyright © 2018 Elsevier Ltd. All rights reserved.

  8. Cryptographic analysis on the key space of optical phase encryption algorithm based on the design of discrete random phase mask

    Science.gov (United States)

    Lin, Chao; Shen, Xueju; Li, Zengyan

    2013-07-01

    The key space of phase encryption algorithm using discrete random phase mask is investigated by numerical simulation in this paper. Random phase mask with finite and discrete phase levels is considered as the core component in most practical optical encryption architectures. The key space analysis is based on the design criteria of discrete random phase mask. The role of random amplitude mask and random phase mask in optical encryption system is identified from the perspective of confusion and diffusion. The properties of discrete random phase mask in a practical double random phase encoding scheme working in both amplitude encoding (AE) and phase encoding (PE) modes are comparably analyzed. The key space of random phase encryption algorithm is evaluated considering both the encryption quality and the brute-force attack resistibility. A method for enlarging the key space of phase encryption algorithm is also proposed to enhance the security of optical phase encryption techniques.

  9. Strategic Dissonance RPA Tactics To Defeat Al Qaeda

    Science.gov (United States)

    2015-11-24

    U.S. refuted the accusations and attempted to appease the critics by increasing operational controls over the approval processes used in executing...of the gratification it received from the targeted strikes without having to commit its own forces, a la Eliot Cohen.28 It did not take long for the...tribal public opinion in the process .33 Had the U.S. and Pakistan been more transparent about the approval process of the RPA strikes initially

  10. Model Uncertainties for Valencia RPA Effect for MINERvA

    Energy Technology Data Exchange (ETDEWEB)

    Gran, Richard [Univ. of Minnesota, Duluth, MN (United States)

    2017-05-08

    This technical note describes the application of the Valencia RPA multi-nucleon effect and its uncertainty to QE reactions from the GENIE neutrino event generator. The analysis of MINERvA neutrino data in Rodrigues et al. PRL 116 071802 (2016) paper makes clear the need for an RPA suppression, especially at very low momentum and energy transfer. That published analysis does not constrain the magnitude of the effect; it only tests models with and without the effect against the data. Other MINERvA analyses need an expression of the model uncertainty in the RPA effect. A well-described uncertainty can be used for systematics for unfolding, for model errors in the analysis of non-QE samples, and as input for fitting exercises for model testing or constraining backgrounds. This prescription takes uncertainties on the parameters in the Valencia RPA model and adds a (not-as-tight) constraint from muon capture data. For MINERvA we apply it as a 2D ($q_0$,$q_3$) weight to GENIE events, in lieu of generating a full beyond-Fermi-gas quasielastic events. Because it is a weight, it can be applied to the generated and fully Geant4 simulated events used in analysis without a special GENIE sample. For some limited uses, it could be cast as a 1D $Q^2$ weight without much trouble. This procedure is a suitable starting point for NOvA and DUNE where the energy dependence is modest, but probably not adequate for T2K or MicroBooNE.

  11. A low and a high energy scissors modes in the two-rotor model and schematic random-phase approximation

    International Nuclear Information System (INIS)

    Iudice, N.L.

    1993-01-01

    It is shown by a model independent numerical estimate that the TRM expression of the M1 strength is fully consistent with the recently discovered saturation properties of the M1 excitations knows as scissors mode

  12. RPA binds histone H3-H4 and functions in DNA replication-coupled nucleosome assembly.

    Science.gov (United States)

    Liu, Shaofeng; Xu, Zhiyun; Leng, He; Zheng, Pu; Yang, Jiayi; Chen, Kaifu; Feng, Jianxun; Li, Qing

    2017-01-27

    DNA replication-coupled nucleosome assembly is essential to maintain genome integrity and retain epigenetic information. Multiple involved histone chaperones have been identified, but how nucleosome assembly is coupled to DNA replication remains elusive. Here we show that replication protein A (RPA), an essential replisome component that binds single-stranded DNA, has a role in replication-coupled nucleosome assembly. RPA directly binds free H3-H4. Assays using a synthetic sequence that mimics freshly unwound single-stranded DNA at replication fork showed that RPA promotes DNA-(H3-H4) complex formation immediately adjacent to double-stranded DNA. Further, an RPA mutant defective in H3-H4 binding exhibited attenuated nucleosome assembly on nascent chromatin. Thus, we propose that RPA functions as a platform for targeting histone deposition to replication fork, through which RPA couples nucleosome assembly with ongoing DNA replication. Copyright © 2017, American Association for the Advancement of Science.

  13. RPA Field Simulations:Dilemma Training for Legal and Ethical Decision Making

    Science.gov (United States)

    2015-11-07

    RPA Field Simulations: Dilemma-Training for Legal and Ethical Decision-Making Professor Wilbur Scott Dept of...Sciences & Leadership all take the Capstone Experience Course (CEC)  CEC offers several different kinds of projects, one consists of RPA Field...Simulation  Two phases in RPA Field Simulation – classroom phase and field phase  Purpose: link theoretical understanding/moral reasoning with

  14. Correlated, Static and Dynamic Polarizabilities of Small Molecules. Comparison of Four "Black Box" Methods

    DEFF Research Database (Denmark)

    Dalskov, Erik K.; Sauer, Stephan P. A.

    1998-01-01

    Molecular static and dynamic polarizabilities for thirteen small molecules have been calculated using four "black box" ab initio methods, the random phase approximation, RPA, the second-order polarization propagator approximation, SOPPA, the second-order polarization propagator approximation...

  15. Dna2 nuclease-helicase structure, mechanism and regulation by Rpa.

    Science.gov (United States)

    Zhou, Chun; Pourmal, Sergei; Pavletich, Nikola P

    2015-11-02

    The Dna2 nuclease-helicase maintains genomic integrity by processing DNA double-strand breaks, Okazaki fragments and stalled replication forks. Dna2 requires ssDNA ends, and is dependent on the ssDNA-binding protein Rpa, which controls cleavage polarity. Here we present the 2.3 Å structure of intact mouse Dna2 bound to a 15-nucleotide ssDNA. The nuclease active site is embedded in a long, narrow tunnel through which the DNA has to thread. The helicase domain is required for DNA binding but not threading. We also present the structure of a flexibly-tethered Dna2-Rpa interaction that recruits Dna2 to Rpa-coated DNA. We establish that a second Dna2-Rpa interaction is mutually exclusive with Rpa-DNA interactions and mediates the displacement of Rpa from ssDNA. This interaction occurs at the nuclease tunnel entrance and the 5' end of the Rpa-DNA complex. Hence, it only displaces Rpa from the 5' but not 3' end, explaining how Rpa regulates cleavage polarity.

  16. Rpa4, a homolog of the 34-kilodalton subunit of the replication protein A complex.

    OpenAIRE

    Keshav, K F; Chen, C; Dutta, A

    1995-01-01

    Replication protein A (RPA) is a complex of three polypeptides of 70, 34, and 13 kDa isolated from diverse eukaryotes. The complex is a single-stranded DNA-binding protein essential for simian virus 40-based DNA replication in vitro and for viability in the yeast Saccharomyces cerevisiae. We have identified a new 30-kDa human protein which interacts with the 70- and 13-kDa subunits of RPA, with a yeast two-hybrid/interaction trap method. This protein, Rpa4, has 47% identity with Rpa2, the 34-...

  17. Reconstitution of RPA-covered single-stranded DNA-activated ATR-Chk1 signaling.

    Science.gov (United States)

    Choi, Jun-Hyuk; Lindsey-Boltz, Laura A; Kemp, Michael; Mason, Aaron C; Wold, Marc S; Sancar, Aziz

    2010-08-03

    ATR kinase is a critical upstream regulator of the checkpoint response to various forms of DNA damage. Previous studies have shown that ATR is recruited via its binding partner ATR-interacting protein (ATRIP) to replication protein A (RPA)-covered single-stranded DNA (RPA-ssDNA) generated at sites of DNA damage where ATR is then activated by TopBP1 to phosphorylate downstream targets including the Chk1 signal transducing kinase. However, this critical feature of the human ATR-initiated DNA damage checkpoint signaling has not been demonstrated in a defined system. Here we describe an in vitro checkpoint system in which RPA-ssDNA and TopBP1 are essential for phosphorylation of Chk1 by the purified ATR-ATRIP complex. Checkpoint defective RPA mutants fail to activate ATR kinase in this system, supporting the conclusion that this system is a faithful representation of the in vivo reaction. Interestingly, we find that an alternative form of RPA (aRPA), which does not support DNA replication, can substitute for the checkpoint function of RPA in vitro, thus revealing a potential role for aRPA in the activation of ATR kinase. We also find that TopBP1 is recruited to RPA-ssDNA in a manner dependent on ATRIP and that the N terminus of TopBP1 is required for efficient recruitment and activation of ATR kinase.

  18. Simultaneous transmission for an encrypted image and a double random-phase encryption key

    Science.gov (United States)

    Yuan, Sheng; Zhou, Xin; Li, Da-Hai; Zhou, Ding-Fu

    2007-06-01

    We propose a method to simultaneously transmit double random-phase encryption key and an encrypted image by making use of the fact that an acceptable decryption result can be obtained when only partial data of the encrypted image have been taken in the decryption process. First, the original image data are encoded as an encrypted image by a double random-phase encryption technique. Second, a double random-phase encryption key is encoded as an encoded key by the Rivest-Shamir-Adelman (RSA) public-key encryption algorithm. Then the amplitude of the encrypted image is modulated by the encoded key to form what we call an encoded image. Finally, the encoded image that carries both the encrypted image and the encoded key is delivered to the receiver. Based on such a method, the receiver can have an acceptable result and secure transmission can be guaranteed by the RSA cipher system.

  19. The random phase transducer in ultrasonic NDT of coarse grain stainless steel

    International Nuclear Information System (INIS)

    Bordier, J.M.; Fink, M.; Le Brun, A.; Cohen-Tenoudji, F.

    1993-11-01

    Ultrasonic NDT of cast stainless steel is known to be difficult due to a huge loss of focussing of the ultrasonic beam, and to a high level speckle noise generated by the coarse grain structure. In this paper, we describe the principle of the ultrasonic random phase transducer. Experimental results are compared with those obtained with a standard spatial compound technique. We show that the random phase transducer is a good tool to characterize the multiple scattering process generated by these materials. (authors). 7 figs., 11 refs

  20. Calculation of the RPA response function of nuclei to quasi-elastic electron scattering with a density-dependent NN interaction

    International Nuclear Information System (INIS)

    Caillon, J-C.; Labarsouque, J.

    1997-01-01

    So far, the non-relativistic longitudinal and transverse functions in electron quasi-elastic scattering on the nuclei failed in reproducing satisfactorily the existent experimental data. The calculations including relativistic RPA correlations utilize until now the relativistic Hartree approximation to describe the nuclear matter. But, this provides an incompressibility module two times higher than its experimental value what is an important drawback for the calculation of realistic relativistic RPA correlations. Hence, we have determined the RPA response functions of nuclei by utilising a description of the relativistic nuclear matter leading to an incompressibility module in agreement with the empirical value. To do that we have utilized an interaction in the relativistic Hartree approximation in which we have determined the coupling constants σ-N and ω-N as a function of the density in order to reproduce the saturation curve obtained by a Dirac-Brueckner calculation. The results which we have obtained show that the longitudinal response function and the Coulomb sum generally overestimated when one utilizes the pure relativistic Hartree approximation, are here in good agreement with the experimental data for several nuclei

  1. PCAF/GCN5-Mediated Acetylation of RPA1 Promotes Nucleotide Excision Repair

    Directory of Open Access Journals (Sweden)

    Meimei Zhao

    2017-08-01

    Full Text Available The RPA complex can integrate multiple stress signals into diverse responses by activating distinct DNA repair pathways. However, it remains unclear how RPA1 elects to activate a specific repair pathway during different types of DNA damage. Here, we report that PCAF/GCN5-mediated K163 acetylation of RPA1 is crucial for nucleotide excision repair (NER but is dispensable for other DNA repair pathways. Mechanistically, we demonstrate that the acetylation of RPA1 is critical for the steady accumulation of XPA at damaged DNA sites and preferentially activates the NER pathway. DNA-PK phosphorylates and activates PCAF upon UV damage and consequently promotes the acetylation of RPA1. Moreover, the acetylation of RPA1 is tightly regulated by HDAC6 and SIRT1. Together, our results demonstrate that the K163 acetylation of RPA1 plays a key role in the repair of UV-induced DNA damage and reveal how the specific RPA1 modification modulates the choice of distinct DNA repair pathways.

  2. Wildlife resource trends in the United States: A technical document supporting the 2000 RPA Assessment

    Science.gov (United States)

    Curtis H. Flather; Stephen J. Brady; Michael S. Knowles

    1999-01-01

    This report documents trends in wildlife resources for the nation as required by the Renewable Resources Planning Act (RPA) of 1974. The report focuses on recent historical trends in wildlife as one indicator of ecosystem health across the United States and updates wildlife trends presented in previous RPA Assessments. The report also shows short- and long-term...

  3. The multi-replication protein A (RPA) system--a new perspective.

    Science.gov (United States)

    Sakaguchi, Kengo; Ishibashi, Toyotaka; Uchiyama, Yukinobu; Iwabata, Kazuki

    2009-02-01

    Replication protein A (RPA) complex has been shown, using both in vivo and in vitro approaches, to be required for most aspects of eukaryotic DNA metabolism: replication, repair, telomere maintenance and homologous recombination. Here, we review recent data concerning the function and biological importance of the multi-RPA complex. There are distinct complexes of RPA found in the biological kingdoms, although for a long time only one type of RPA complex was believed to be present in eukaryotes. Each complex probably serves a different role. In higher plants, three distinct large and medium subunits are present, but only one species of the smallest subunit. Each of these protein subunits forms stable complexes with their respective partners. They are paralogs as complex. Humans possess two paralogs and one analog of RPA. The multi-RPA system can be regarded as universal in eukaryotes. Among eukaryotic kingdoms, paralogs, orthologs, analogs and heterologs of many DNA synthesis-related factors, including RPA, are ubiquitous. Convergent evolution seems to be ubiquitous in these processes. Using recent findings, we review the composition and biological functions of RPA complexes.

  4. Elevated level of human RPA interacting protein α (hRIPα) in cervical tumor cells is involved in cell proliferation through regulating RPA transport.

    Science.gov (United States)

    Namkoong, Sim; Lee, Eun-Ju; Jang, Ik-Soon; Park, Junsoo

    2012-10-19

    Replication protein A (RPA) is a eukaryotic single-stranded DNA binding protein that is essential for DNA replication, repair, and recombination, and human RPA interacting protein α (hRIPα) is the nuclear transporter of RPA. Here, we report the regulatory role of hRIPα protein in cell proliferation. Western blot analysis revealed that the level of hRIPα was frequently elevated in cervical tumors tissues and hRIPα knockdown by siRNA inhibited cellular proliferation through deregulation of the cell cycle. In addition, overexpression of hRIPα resulted in increased clonogenicity. These results indicate that hRIPα is involved in cell proliferation through regulation of RPA transport. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  5. Divergent Roles of RPA Homologs of the Model Archaeon Halobacterium salinarum in Survival of DNA Damage.

    Science.gov (United States)

    Evans, Jessica J; Gygli, Patrick E; McCaskill, Julienne; DeVeaux, Linda C

    2018-04-20

    The haloarchaea are unusual in possessing genes for multiple homologs to the ubiquitous single-stranded DNA binding protein (SSB or replication protein A, RPA) found in all three domains of life. Halobacterium salinarum contains five homologs: two are eukaryotic in organization, two are prokaryotic and are encoded on the minichromosomes, and one is uniquely euryarchaeal. Radiation-resistant mutants previously isolated show upregulation of one of the eukaryotic-type RPA genes. Here, we have created deletions in the five RPA operons. These deletion mutants were exposed to DNA-damaging conditions: ionizing radiation, UV radiation, and mitomycin C. Deletion of the euryarchaeal homolog, although not lethal as in Haloferax volcanii , causes severe sensitivity to all of these agents. Deletion of the other RPA/SSB homologs imparts a variable sensitivity to these DNA-damaging agents, suggesting that the different RPA homologs have specialized roles depending on the type of genomic insult encountered.

  6. Self-consistent RPA and the time-dependent density matrix approach

    Energy Technology Data Exchange (ETDEWEB)

    Schuck, P. [Institut de Physique Nucleaire, Orsay (France); CNRS et Universite Joseph Fourier, Laboratoire de Physique et Modelisation des Milieux Condenses, Grenoble (France); Tohyama, M. [Kyorin University School of Medicine, Mitaka, Tokyo (Japan)

    2016-10-15

    The time-dependent density matrix (TDDM) or BBGKY (Bogoliubov, Born, Green, Kirkwood, Yvon) approach is decoupled and closed at the three-body level in finding a natural representation of the latter in terms of a quadratic form of two-body correlation functions. In the small amplitude limit an extended RPA coupled to an also extended second RPA is obtained. Since including two-body correlations means that the ground state cannot be a Hartree-Fock state, naturally the corresponding RPA is upgraded to Self-Consistent RPA (SCRPA) which was introduced independently earlier and which is built on a correlated ground state. SCRPA conserves all the properties of standard RPA. Applications to the exactly solvable Lipkin and the 1D Hubbard models show good performances of SCRPA and TDDM. (orig.)

  7. Projecting climate change in the United States: A technical document supporting the Forest Service RPA 2010 Assessment

    Science.gov (United States)

    Linda A. Joyce; David T. Price; David P. Coulson; Daniel W. McKenney; R. Martin Siltanen; Pia Papadopol; Kevin. Lawrence

    2014-01-01

    A set of climate change projections for the United States was developed for use in the 2010 USDA Forest Service RPA Assessment. These climate projections, along with projections for population dynamics, economic growth, and land use change in the United States, comprise the RPA scenarios and are used in the RPA Assessment to project future renewable resource conditions...

  8. Impulse attack-free four random phase mask encryption based on a 4-f optical system.

    Science.gov (United States)

    Kumar, Pramod; Joseph, Joby; Singh, Kehar

    2009-04-20

    Optical encryption methods based on double random phase encryption (DRPE) have been shown to be vulnerable to different types of attacks. The Fourier plane random phase mask (RPM), which is the most important key, can be cracked with a single impulse function attack. Such an attack is viable because the Fourier transform of a delta function is a unity function. Formation of a unity function can be avoided if RPMs are placed in front of both lenses in a 4-f optical setup, thereby protecting the DRPE from an impulse attack. We have performed numerical simulations to verify the proposed scheme. Resistance of this scheme is checked against the brute force and the impulse function attacks. The experimental results validate the feasibility of the scheme.

  9. Key management of the double random-phase-encoding method using public-key encryption

    Science.gov (United States)

    Saini, Nirmala; Sinha, Aloka

    2010-03-01

    Public-key encryption has been used to encode the key of the encryption process. In the proposed technique, an input image has been encrypted by using the double random-phase-encoding method using extended fractional Fourier transform. The key of the encryption process have been encoded by using the Rivest-Shamir-Adelman (RSA) public-key encryption algorithm. The encoded key has then been transmitted to the receiver side along with the encrypted image. In the decryption process, first the encoded key has been decrypted using the secret key and then the encrypted image has been decrypted by using the retrieved key parameters. The proposed technique has advantage over double random-phase-encoding method because the problem associated with the transmission of the key has been eliminated by using public-key encryption. Computer simulation has been carried out to validate the proposed technique.

  10. Choice of optical system is critical for the security of double random phase encryption systems

    Science.gov (United States)

    Muniraj, Inbarasan; Guo, Changliang; Malallah, Ra'ed; Cassidy, Derek; Zhao, Liang; Ryle, James P.; Healy, John J.; Sheridan, John T.

    2017-06-01

    The linear canonical transform (LCT) is used in modeling a coherent light-field propagation through first-order optical systems. Recently, a generic optical system, known as the quadratic phase encoding system (QPES), for encrypting a two-dimensional image has been reported. In such systems, two random phase keys and the individual LCT parameters (α,β,γ) serve as secret keys of the cryptosystem. It is important that such encryption systems also satisfy some dynamic security properties. We, therefore, examine such systems using two cryptographic evaluation methods, the avalanche effect and bit independence criterion, which indicate the degree of security of the cryptographic algorithms using QPES. We compared our simulation results with the conventional Fourier and the Fresnel transform-based double random phase encryption (DRPE) systems. The results show that the LCT-based DRPE has an excellent avalanche and bit independence characteristics compared to the conventional Fourier and Fresnel-based encryption systems.

  11. A novel attack method about double-random-phase-encoding-based image hiding method

    Science.gov (United States)

    Xu, Hongsheng; Xiao, Zhijun; Zhu, Xianchen

    2018-03-01

    By using optical image processing techniques, a novel text encryption and hiding method applied by double-random phase-encoding technique is proposed in the paper. The first step is that the secret message is transformed into a 2-dimension array. The higher bits of the elements in the array are used to fill with the bit stream of the secret text, while the lower bits are stored specific values. Then, the transformed array is encoded by double random phase encoding technique. Last, the encoded array is embedded on a public host image to obtain the image embedded with hidden text. The performance of the proposed technique is tested via analytical modeling and test data stream. Experimental results show that the secret text can be recovered either accurately or almost accurately, while maintaining the quality of the host image embedded with hidden data by properly selecting the method of transforming the secret text into an array and the superimposition coefficient.

  12. Self-consistent Hartree-Fock RPA calculations in 208Pb

    Science.gov (United States)

    Taqi, Ali H.; Ali, Mohammed S.

    2018-01-01

    The nuclear structure of 208Pb is studied in the framework of the self-consistent random phase approximation (SCRPA). The Hartree-Fock mean field and single particle states are used to implement a completely SCRPA with Skyrme-type interactions. The Hamiltonian is diagonalised within a model space using five Skyrme parameter sets, namely LNS, SkI3, SkO, SkP and SLy4. In view of the huge number of the existing Skyrme-force parameterizations, the question remains which of them provide the best description of data. The approach attempts to accurately describe the structure of the spherical even-even nucleus 208Pb. To illustrate our approach, we compared the binding energy, charge density distribution, excitation energy levels scheme with the available experimental data. Moreover, we calculated isoscalar and isovector monopole, dipole, and quadrupole transition densities and strength functions.

  13. Improved light extraction from white organic light-emitting devices using a binary random phase array

    Energy Technology Data Exchange (ETDEWEB)

    Inada, Yasuhisa, E-mail: inada.yasuhisa@jp.panasonic.com; Nishiwaki, Seiji; Hirasawa, Taku; Nakamura, Yoshitaka; Hashiya, Akira; Wakabayashi, Shin-ichi; Suzuki, Masa-aki [R and D Division, Panasonic Corporation, 1006 Kadoma, Kadoma City, Osaka 571-8501 (Japan); Matsuzaki, Jumpei [Device Development Center, Eco Solutions Company, Panasonic Corporation, 1048 Kadoma, Osaka 571-8686 Japan (Japan)

    2014-02-10

    We have developed a binary random phase array (BRPA) to improve the light extraction performance of white organic light-emitting devices (WOLEDs). We demonstrated that the scattering of incoming light can be controlled by employing diffraction optics to modify the structural parameters of the BRPA. Applying a BRPA to the substrate of the WOLED leads to enhanced extraction efficiency and suppression of angle-dependent color changes. Our systematic study clarifies the effect of scattering on the light extraction of WOLEDs.

  14. Improved light extraction from white organic light-emitting devices using a binary random phase array

    International Nuclear Information System (INIS)

    Inada, Yasuhisa; Nishiwaki, Seiji; Hirasawa, Taku; Nakamura, Yoshitaka; Hashiya, Akira; Wakabayashi, Shin-ichi; Suzuki, Masa-aki; Matsuzaki, Jumpei

    2014-01-01

    We have developed a binary random phase array (BRPA) to improve the light extraction performance of white organic light-emitting devices (WOLEDs). We demonstrated that the scattering of incoming light can be controlled by employing diffraction optics to modify the structural parameters of the BRPA. Applying a BRPA to the substrate of the WOLED leads to enhanced extraction efficiency and suppression of angle-dependent color changes. Our systematic study clarifies the effect of scattering on the light extraction of WOLEDs

  15. RPA coordinates DNA end resection and prevents formation of DNA hairpins.

    Science.gov (United States)

    Chen, Huan; Lisby, Michael; Symington, Lorraine S

    2013-05-23

    Replication protein A (RPA) is an essential eukaryotic single-stranded DNA binding protein with a central role in DNA metabolism. RPA directly participates in DNA double-strand break repair by stimulating 5'-3' end resection by the Sgs1/BLM helicase and Dna2 endonuclease in vitro. Here we investigated the role of RPA in end resection in vivo, using a heat-inducible degron system that allows rapid conditional depletion of RPA in Saccharomyces cerevisiae. We found that RPA depletion eliminated both the Sgs1-Dna2- and Exo1-dependent extensive resection pathways and synergized with mre11Δ to prevent end resection. The short single-stranded DNA tails formed in the absence of RPA were unstable due to 3' strand loss and the formation of fold-back hairpin structures that required resection initiation and Pol32-dependent DNA synthesis. Thus, RPA is required to generate ssDNA, and also to protect ssDNA from degradation and inappropriate annealing that could lead to genome rearrangements. Copyright © 2013 Elsevier Inc. All rights reserved.

  16. RING finger and WD repeat domain 3 (RFWD3) associates with replication protein A (RPA) and facilitates RPA-mediated DNA damage response.

    Science.gov (United States)

    Liu, Shangfeng; Chu, Jessica; Yucer, Nur; Leng, Mei; Wang, Shih-Ya; Chen, Benjamin P C; Hittelman, Walter N; Wang, Yi

    2011-06-24

    DNA damage response is crucial for maintaining genomic integrity and preventing cancer by coordinating the activation of checkpoints and the repair of damaged DNA. Central to DNA damage response are the two checkpoint kinases ATM and ATR that phosphorylate a wide range of substrates. RING finger and WD repeat domain 3 (RFWD3) was initially identified as a substrate of ATM/ATR from a proteomic screen. Subsequent studies showed that RFWD3 is an E3 ubiquitin ligase that ubiquitinates p53 in vitro and positively regulates p53 levels in response to DNA damage. We report here that RFWD3 associates with replication protein A (RPA), a single-stranded DNA-binding protein that plays essential roles in DNA replication, recombination, and repair. Binding of RPA to single-stranded DNA (ssDNA), which is generated by DNA damage and repair, is essential for the recruitment of DNA repair factors to damaged sites and the activation of checkpoint signaling. We show that RFWD3 is physically associated with RPA and rapidly localizes to sites of DNA damage in a RPA-dependent manner. In vitro experiments suggest that the C terminus of RFWD3, which encompass the coiled-coil domain and the WD40 domain, is necessary for binding to RPA. Furthermore, DNA damage-induced phosphorylation of RPA and RFWD3 is dependent upon each other. Consequently, loss of RFWD3 results in the persistent foci of DNA damage marker γH2AX and the repair protein Rad51 in damaged cells. These findings suggest that RFWD3 is recruited to sites of DNA damage and facilitates RPA-mediated DNA damage signaling and repair.

  17. RPA mediates recombination repair during replication stress and is displaced from DNA by checkpoint signalling in human cells

    DEFF Research Database (Denmark)

    Sleeth, Kate M; Sørensen, Claus Storgaard; Issaeva, Natalia

    2007-01-01

    The replication protein A (RPA) is involved in most, if not all, nuclear metabolism involving single-stranded DNA. Here, we show that RPA is involved in genome maintenance at stalled replication forks by the homologous recombination repair system in humans. Depletion of the RPA protein inhibited...... the formation of RAD51 nuclear foci after hydroxyurea-induced replication stalling leading to persistent unrepaired DNA double-strand breaks (DSBs). We demonstrate a direct role of RPA in homology directed recombination repair. We find that RPA is dispensable for checkpoint kinase 1 (Chk1) activation...... and that RPA directly binds RAD52 upon replication stress, suggesting a direct role in recombination repair. In addition we show that inhibition of Chk1 with UCN-01 decreases dissociation of RPA from the chromatin and inhibits association of RAD51 and RAD52 with DNA. Altogether, our data suggest a direct role...

  18. Lensless digital holography with diffuse illumination through a pseudo-random phase mask.

    Science.gov (United States)

    Bernet, Stefan; Harm, Walter; Jesacher, Alexander; Ritsch-Marte, Monika

    2011-12-05

    Microscopic imaging with a setup consisting of a pseudo-random phase mask, and an open CMOS camera, without an imaging objective, is demonstrated. The pseudo random phase mask acts as a diffuser for an incoming laser beam, scattering a speckle pattern to a CMOS chip, which is recorded once as a reference. A sample which is afterwards inserted somewhere in the optical beam path changes the speckle pattern. A single (non-iterative) image processing step, comparing the modified speckle pattern with the previously recorded one, generates a sharp image of the sample. After a first calibration the method works in real-time and allows quantitative imaging of complex (amplitude and phase) samples in an extended three-dimensional volume. Since no lenses are used, the method is free from lens abberations. Compared to standard inline holography the diffuse sample illumination improves the axial sectioning capability by increasing the effective numerical aperture in the illumination path, and it suppresses the undesired so-called twin images. For demonstration, a high resolution spatial light modulator (SLM) is programmed to act as the pseudo-random phase mask. We show experimental results, imaging microscopic biological samples, e.g. insects, within an extended volume at a distance of 15 cm with a transverse and longitudinal resolution of about 60 μm and 400 μm, respectively.

  19. Two fast temperature sensors for probing of the atmospheric boundary layer using small remotely piloted aircraft (RPA

    Directory of Open Access Journals (Sweden)

    N. Wildmann

    2013-08-01

    Full Text Available Two types of temperature sensors are designed and tested: a thermocouple and a fine wire resistance thermometer. The intention of this study is to figure out which kind of measurement principle is in general more suited for atmospheric boundary layer meteorology with small remotely piloted aircraft (RPA. The sensors are calibrated in a NIST traceable climate chamber and validated in flight against tower measurements, radiosondes and remote sensing. The sensors have a measurement range of at least −10–50 °C, an absolute RMS error of less than ±0.2 K which is stable over the lifetime of the sensors, and a resolution of about 0.01 K. Both devices are tested for typical errors like radiation error and adiabatic heating, as well as for their dynamic response. Spectral resolutions of up to approximately 10 Hz can be obtained with both sensors, which makes them suitable for turbulence measurement. Their low cost of less than 100 EUR in pure hardware is a major advantage for research with small RPA.

  20. Two fast temperature sensors for probing of the atmospheric boundary layer using small remotely piloted aircraft (RPA)

    Science.gov (United States)

    Wildmann, N.; Mauz, M.; Bange, J.

    2013-08-01

    Two types of temperature sensors are designed and tested: a thermocouple and a fine wire resistance thermometer. The intention of this study is to figure out which kind of measurement principle is in general more suited for atmospheric boundary layer meteorology with small remotely piloted aircraft (RPA). The sensors are calibrated in a NIST traceable climate chamber and validated in flight against tower measurements, radiosondes and remote sensing. The sensors have a measurement range of at least -10-50 °C, an absolute RMS error of less than ±0.2 K which is stable over the lifetime of the sensors, and a resolution of about 0.01 K. Both devices are tested for typical errors like radiation error and adiabatic heating, as well as for their dynamic response. Spectral resolutions of up to approximately 10 Hz can be obtained with both sensors, which makes them suitable for turbulence measurement. Their low cost of less than 100 EUR in pure hardware is a major advantage for research with small RPA.

  1. Approximate Likelihood

    CERN Multimedia

    CERN. Geneva

    2015-01-01

    Most physics results at the LHC end in a likelihood ratio test. This includes discovery and exclusion for searches as well as mass, cross-section, and coupling measurements. The use of Machine Learning (multivariate) algorithms in HEP is mainly restricted to searches, which can be reduced to classification between two fixed distributions: signal vs. background. I will show how we can extend the use of ML classifiers to distributions parameterized by physical quantities like masses and couplings as well as nuisance parameters associated to systematic uncertainties. This allows for one to approximate the likelihood ratio while still using a high dimensional feature vector for the data. Both the MEM and ABC approaches mentioned above aim to provide inference on model parameters (like cross-sections, masses, couplings, etc.). ABC is fundamentally tied Bayesian inference and focuses on the “likelihood free” setting where only a simulator is available and one cannot directly compute the likelihood for the dat...

  2. Diophantine approximation

    CERN Document Server

    Schmidt, Wolfgang M

    1980-01-01

    "In 1970, at the U. of Colorado, the author delivered a course of lectures on his famous generalization, then just established, relating to Roth's theorem on rational approxi- mations to algebraic numbers. The present volume is an ex- panded and up-dated version of the original mimeographed notes on the course. As an introduction to the author's own remarkable achievements relating to the Thue-Siegel-Roth theory, the text can hardly be bettered and the tract can already be regarded as a classic in its field."(Bull.LMS) "Schmidt's work on approximations by algebraic numbers belongs to the deepest and most satisfactory parts of number theory. These notes give the best accessible way to learn the subject. ... this book is highly recommended." (Mededelingen van het Wiskundig Genootschap)

  3. Solving the RPA eigenvalue equation in real-space

    CERN Document Server

    Muta, A; Hashimoto, Y; Yabana, K

    2002-01-01

    We present a computational method to solve the RPA eigenvalue equation employing a uniform grid representation in three-dimensional Cartesian coordinates. The conjugate gradient method is used for this purpose as an interactive method for a generalized eigenvalue problem. No construction of unoccupied orbitals is required in the procedure. We expect this method to be useful for systems lacking spatial symmetry to calculate accurate eigenvalues and transition matrix elements of a few low-lying excitations. Some applications are presented to demonstrate the feasibility of the method, considering the simplified mean-field model as an example of a nuclear physics system and the electronic excitations in molecules with time-dependent density functional theory as an example of an electronic system. (author)

  4. Stability of thermal HFB and dissipative thermal RPA

    CERN Document Server

    Tanabe, K

    1999-01-01

    It is shown that, as for a Nilsson + pairing model, the extended stability condition of the thermal Hartree-Fock-Bogoliubov (THFB) solution coincides with the one of the thermal RPA (TRPA) solution unless the pairing constant G is too large. As possible extensions of the TRPA equation in alternative ways describing thermal fluctuation effect, the extended TRPA (ETRPA) and the dissipative TRPA (DTRPA) are discussed. Furthermore, the general microscopic framework of the TRPA predicts the saturation and decrease of giant resonance width in high temperature limit, i.e. the fragmentation width GAMMA sub f propor to(kT) sup ( sup - sup 3 sup ( sup 2 sup ) sup ) and the spreading width GAMMA suparrow down propor to(kT) sup ( sup - sup 1 sup ( sup 2 sup ) sup ).

  5. Using a short-pulse diffraction-limited laser beam to probe filamentation of a random phase plate smoothed beam.

    Science.gov (United States)

    Kline, J L; Montgomery, D S; Flippo, K A; Johnson, R P; Rose, H A; Shimada, T; Williams, E A

    2008-10-01

    A short pulse (few picoseconds) laser probe provides high temporal resolution measurements to elucidate details of fast dynamic phenomena not observable with typical longer laser pulse probes and gated diagnostics. Such a short pulse laser probe (SPLP) has been used to measure filamentation of a random phase plate (RPP) smoothed laser beam in a gas-jet plasma. The plasma index of refraction due to driven density and temperature fluctuations by the RPP beam perturbs the phase front of a SPLP propagating at a 90 degree angle with respect to the RPP interaction beam. The density and temperature fluctuations are quasistatic on the time scale of the SPLP (approximately 2 ps). The transmitted near-field intensity distribution from the SPLP provides a measure of the phase front perturbation. At low plasma densities, the transmitted intensity pattern is asymmetric with striations across the entire probe beam in the direction of the RPP smoothed beam. As the plasma density increases, the striations break up into smaller sizes along the direction of the RPP beam propagation. The breakup of the intensity pattern is consistent with self-focusing of the RPP smoothed interaction beam. Simulations of the experiment using the wave propagation code, PF3D, are in qualitative agreement demonstrating that the asymmetric striations can be attributed to the RPP driven density fluctuations. Quantification of the beam breakup measured by the transmitted SPLP could lead to a new method for measuring self-focusing of lasers in underdense plasmas.

  6. Civil mini-RPA's for the 1980's: Avionics design considerations. [remotely piloted vehicles

    Science.gov (United States)

    Karmarkar, J. S.

    1975-01-01

    A number of remote sensing or surveillance tasks (e.g., fire fighting, crop monitoring) in the civilian sector of our society may be performed in a cost effective manner by use of small remotely piloted aircraft (RPA). This study was conducted to determine equipment (and the associated technology) that is available, and that could be applied to the mini-RPA and to examine the potential applications of the mini-RPA with special emphasis on the wild fire surveillance mission. The operational considerations of using the mini-RPA as affected by government regulatory agencies were investigated. These led to equipment requirements (e.g., infra-red sensors) over and above those for the performance of the mission. A computer technology survey and forecast was performed. Key subsystems were identified, and a distributed microcomputer configuration, that was functionally modular, was recommended. Areas for further NASA research and development activity were also identified.

  7. Interventional closure of RPA-to-LA communication in an oligosymptomatic neonate.

    Science.gov (United States)

    Benz, Dominik C; Burkhardt, Barbara; Quandt, Daniel; Stambach, Dominik; Knirsch, Walter; Kretschmar, Oliver

    2014-12-01

    Direct communication between the right pulmonary artery (RPA) and the left atrium (LA) is a very rare cardiac malformation. Clinical presentation of RPA-to-LA communication depends on the size of the communication, the amount of right-to-left shunt, the patient's age, and pulmonary vascular resistance. Patients with small communications usually present oligosymptomatic and are diagnosed at an older age. A delay of diagnosis bears the risk of severe complications and needs to be prevented by proper work-up of oligosymptomatic neonates. Treatment of RPA-to-LA communications used to be performed by surgical closure, and the interventional approach has only been established as a less invasive alternative in recent years. Although patients with small RPA-to-LA communications usually present oligosymptomatic, early diagnosis and treatment is essential to prevent life-threatening complications.

  8. RFWD3-Dependent Ubiquitination of RPA Regulates Repair at Stalled Replication Forks.

    Science.gov (United States)

    Elia, Andrew E H; Wang, David C; Willis, Nicholas A; Boardman, Alexander P; Hajdu, Ildiko; Adeyemi, Richard O; Lowry, Elizabeth; Gygi, Steven P; Scully, Ralph; Elledge, Stephen J

    2015-10-15

    We have used quantitative proteomics to profile ubiquitination in the DNA damage response (DDR). We demonstrate that RPA, which functions as a protein scaffold in the replication stress response, is multiply ubiquitinated upon replication fork stalling. Ubiquitination of RPA occurs on chromatin, involves sites outside its DNA binding channel, does not cause proteasomal degradation, and increases under conditions of fork collapse, suggesting a role in repair at stalled forks. We demonstrate that the E3 ligase RFWD3 mediates RPA ubiquitination. RFWD3 is necessary for replication fork restart, normal repair kinetics during replication stress, and homologous recombination (HR) at stalled replication forks. Mutational analysis suggests that multisite ubiquitination of the entire RPA complex is responsible for repair at stalled forks. Multisite protein group sumoylation is known to promote HR in yeast. Our findings reveal a similar requirement for multisite protein group ubiquitination during HR at stalled forks in mammalian cells. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. Evaluation of the effect of RFCA in patients with WPW syndrome using RPA

    International Nuclear Information System (INIS)

    Zhang Wei; Dong Shenan; Jiang Yimin

    1996-01-01

    Whether radionuclide phase analysis (RPA) could evaluate the effect of radiofrequency current ablation (RFCA) in patients with Wolff-Parkinson-White (WPW) syndrome was evaluated. 18 patients with WPW syndrome were studied using RPA pre- and post-RFCA. RPA identified the sites of pre-excitation in all patients before RFCA. Compared with the pre-RFCA study, the sites of pre-excitation disappeared in 12 cases, disappeared gradually in 4 cases and unchanged in 2 cases. 50 RFCA was successful in the former two patterns, but failed in the last pattern. RPA can evaluate the changes of pre-excitation sites in patients with WPW syndrome before and after RFCA. It was a noninvasive and reliable method for assessing and monitoring the effect of RFCA in patients with WPW syndrome

  10. Replication-mediated disassociation of replication protein A-XPA complex upon DNA damage: implications for RPA handing off.

    Science.gov (United States)

    Jiang, Gaofeng; Zou, Yue; Wu, Xiaoming

    2012-08-01

    RPA (replication protein A), the eukaryotic ssDNA (single-stranded DNA)-binding protein, participates in most cellular processes in response to genotoxic insults, such as NER (nucleotide excision repair), DNA, DSB (double-strand break) repair and activation of cell cycle checkpoint signalling. RPA interacts with XPA (xeroderma pigmentosum A) and functions in early stage of NER. We have shown that in cells the RPA-XPA complex disassociated upon exposure of cells to high dose of UV irradiation. The dissociation required replication stress and was partially attributed to tRPA hyperphosphorylation. Treatment of cells with CPT (camptothecin) and HU (hydroxyurea), which cause DSB DNA damage and replication fork collapse respectively and also leads to the disruption of RPA-XPA complex. Purified RPA and XPA were unable to form complex in vitro in the presence of ssDNA. We propose that the competition-based RPA switch among different DNA metabolic pathways regulates the dissociation of RPA with XPA in cells after DNA damage. The biological significances of RPA-XPA complex disruption in relation with checkpoint activation, DSB repair and RPA hyperphosphorylation are discussed.

  11. Validation of the RTOG recursive partitioning analysis (RPA) classification for brain metastases

    International Nuclear Information System (INIS)

    Gaspar, Laurie E.; Scott, Charles; Murray, Kevin; Curran, Walter

    2000-01-01

    Purpose: The Radiation Therapy Oncology Group (RTOG) previously developed three prognostic classes for brain metastases using recursive partitioning analysis (RPA) of a large database. These classes were based on Karnofsky performance status (KPS), primary tumor status, presence of extracranial system metastases, and age. An analysis of RTOG 91-04, a randomized study comparing two dose-fractionation schemes with a comparison to the established RTOG database, was considered important to validate the RPA classes. Methods and Materials: A total of 445 patients were randomized on RTOG 91-04, a Phase III study of accelerated hyperfractionation versus accelerated fractionation. No difference was observed between the two treatment arms with respect to survival. Four hundred thirty-two patients were included in this analysis. The majority of the patients were under age 65, had KPS 70-80, primary tumor controlled, and brain-only metastases. The initial RPA had three classes, but only patients in RPA Classes I and II were eligible for RTOG 91-04. Results: For RPA Class I, the median survival time was 6.2 months and 7.1 months for 91-04 and the database, respectively. The 1-year survival was 29% for 91-04 versus 32% for the database. There was no significant difference in the two survival distributions (p = 0.72). For RPA Class II, the median survival time was 3.8 months for 91-04 versus 4.2 months for the database. The 1-year survival was 12% and 16% for 91-04 and the database, respectively (p = 0.22). Conclusion: This analysis indicates that the RPA classes are valid and reliable for historical comparisons. Both the RTOG and other clinical trial organizers should currently utilize this RPA classification as a stratification factor for clinical trials

  12. Microarray data analyses of yeast RNA Pol I subunit RPA12 deletion strain

    Directory of Open Access Journals (Sweden)

    Kamlesh Kumar Yadav

    2016-06-01

    Full Text Available The ribosomal RNA (rRNA biosynthesis is the most energy consuming process in all living cells and the majority of total transcription activity is dedicated for synthesizing rRNA. The cells may adjust the synthesis of rRNA with the availability of resources. rRNA is mainly synthesized by RNA polymerase I that is composed of 14 subunits. Deletion of RPA12, 14, 39 and 49 are viable. RPA12 is a very small protein (13.6 kDa, and the amount of protein in the cells is very high (12,000 molecules per cell, but the role of this protein is unknown in other cellular metabolic processes (Kulak et al., 2014 [1]. RPA12 consists of two zinc-binding domains and it is required for the termination of rRNA synthesis (Mullem et al., 2002 [2]. Deletions of RPA12 in Saccharomyces cerevisiae and Schizosaccharomyces pombe cause a conditional growth defect (Nogi et al., 1993 [3]. In S. pombe, C-terminal deletion behaves like wild-type (Imazawa et al., 2001 [4]. This prompted us to investigate in detail the physiological role of RPA12 in S. cerevisiae, we performed the microarray of rpa12∆ strain and deposited into Gene Expression Omnibus under GSE68731. The analysis of microarray data revealed that the expression of major cellular metabolism genes is high. The amino acid biosynthesis, nonpolar lipid biosynthesis and glucose metabolic genes are highly expressed. The analyses also revealed that the rpa12∆ cells have an uncontrolled synthesis of cell metabolites, so RPA12 could be a master regulator for whole cellular metabolism.

  13. RPA-mediated unfolding of systematically varying G-quadruplex structures.

    Science.gov (United States)

    Ray, Sujay; Qureshi, Mohammad H; Malcolm, Dominic W; Budhathoki, Jagat B; Celik, Uğur; Balci, Hamza

    2013-05-21

    G-quadruplex (GQ) is a noncanonical nucleic acid structure that is formed by guanine rich sequences. Unless it is destabilized by proteins such as replication protein A (RPA), GQ could interfere with DNA metabolic functions, such as replication or repair. We studied RPA-mediated GQ unfolding using single-molecule FRET on two groups of GQ structures that have different loop lengths and different numbers of G-tetrad layers. We observed a linear increase in the steady-state stability of the GQ against RPA-mediated unfolding with increasing number of layers or decreasing loop length. The stability demonstrated by different GQ structures varied by at least three orders of magnitude. Those with shorter loops (less than three nucleotides long) or a greater number of layers (more than three layers) maintained a significant folded population even at physiological RPA concentration (≈1 μM), raising the possibility of physiological viability of such GQ structures. Finally, we measured the transition time between the start and end of the RPA-mediated GQ unfolding process to be 0.35 ± 0.10 s for all GQ constructs we studied, despite significant differences in their steady-state stabilities. We propose a two-step RPA-mediated GQ unfolding mechanism that is consistent with our observations. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  14. Oxidative Damage to RPA Limits the Nucleotide Excision Repair Capacity of Human Cells.

    Science.gov (United States)

    Guven, Melisa; Brem, Reto; Macpherson, Peter; Peacock, Matthew; Karran, Peter

    2015-11-01

    Nucleotide excision repair (NER) protects against sunlight-induced skin cancer. Defective NER is associated with photosensitivity and a high skin cancer incidence. Some clinical treatments that cause photosensitivity can also increase skin cancer risk. Among these, the immunosuppressant azathioprine and the fluoroquinolone antibiotics ciprofloxacin and ofloxacin interact with UVA radiation to generate reactive oxygen species that diminish NER capacity by causing protein damage. The replication protein A (RPA) DNA-binding protein has a pivotal role in DNA metabolism and is an essential component of NER. The relationship between protein oxidation and NER inhibition was investigated in cultured human cells expressing different levels of RPA. We show here that RPA is limiting for NER and that oxidative damage to RPA compromises NER capability. Our findings reveal that cellular RPA is surprisingly vulnerable to oxidation, and we identify oxidized forms of RPA that are associated with impaired NER. The vulnerability of NER to inhibition by oxidation provides a connection between cutaneous photosensitivity, protein damage, and increased skin cancer risk. Our findings emphasize that damage to DNA repair proteins, as well as to DNA itself, is likely to be an important contributor to skin cancer risk.

  15. Promotion of BRCA2-Dependent Homologous Recombination by DSS1 via RPA Targeting and DNA Mimicry.

    Science.gov (United States)

    Zhao, Weixing; Vaithiyalingam, Sivaraja; San Filippo, Joseph; Maranon, David G; Jimenez-Sainz, Judit; Fontenay, Gerald V; Kwon, Youngho; Leung, Stanley G; Lu, Lucy; Jensen, Ryan B; Chazin, Walter J; Wiese, Claudia; Sung, Patrick

    2015-07-16

    The tumor suppressor BRCA2 is thought to facilitate the handoff of ssDNA from replication protein A (RPA) to the RAD51 recombinase during DNA break and replication fork repair by homologous recombination. However, we find that RPA-RAD51 exchange requires the BRCA2 partner DSS1. Biochemical, structural, and in vivo analyses reveal that DSS1 allows the BRCA2-DSS1 complex to physically and functionally interact with RPA. Mechanistically, DSS1 acts as a DNA mimic to attenuate the affinity of RPA for ssDNA. A mutation in the solvent-exposed acidic domain of DSS1 compromises the efficacy of RPA-RAD51 exchange. Thus, by targeting RPA and mimicking DNA, DSS1 functions with BRCA2 in a two-component homologous recombination mediator complex in genome maintenance and tumor suppression. Our findings may provide a paradigm for understanding the roles of DSS1 in other biological processes. Copyright © 2015 Elsevier Inc. All rights reserved.

  16. Annealing helicase HARP closes RPA-stabilized DNA bubbles non-processively.

    Science.gov (United States)

    Burnham, Daniel R; Nijholt, Bas; De Vlaminck, Iwijn; Quan, Jinhua; Yusufzai, Timur; Dekker, Cees

    2017-05-05

    We investigate the mechanistic nature of the Snf2 family protein HARP, mutations of which are responsible for Schimke immuno-osseous dysplasia. Using a single-molecule magnetic tweezers assay, we construct RPA-stabilized DNA bubbles within torsionally constrained DNA to investigate the annealing action of HARP on a physiologically relevant substrate. We find that HARP closes RPA-stabilized bubbles in a slow reaction, taking on the order of tens of minutes for ∼600 bp of DNA to be re-annealed. The data indicate that DNA re-anneals through the removal of RPA, which is observed as clear steps in the bubble-closing traces. The dependence of the closing rate on both ionic strength and HARP concentration indicates that removal of RPA occurs via an association-dissociation mechanism where HARP does not remain associated with the DNA. The enzyme exhibits classical Michaelis-Menten kinetics and acts cooperatively with a Hill coefficient of 3 ± 1. Our work also allows the determination of some important features of RPA-bubble structures at low supercoiling, including the existence of multiple bubbles and that RPA molecules are mis-registered on the two strands. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. Replication Protein A (RPA) deficiency activates the Fanconi anemia DNA repair pathway.

    Science.gov (United States)

    Jang, Seok-Won; Jung, Jin Ki; Kim, Jung Min

    2016-09-01

    The Fanconi anemia (FA) pathway regulates DNA inter-strand crosslink (ICL) repair. Despite our greater understanding of the role of FA in ICL repair, its function in the preventing spontaneous genome instability is not well understood. Here, we show that depletion of replication protein A (RPA) activates the FA pathway. RPA1 deficiency increases chromatin recruitment of FA core complex, leading to FANCD2 monoubiquitination (FANCD2-Ub) and foci formation in the absence of DNA damaging agents. Importantly, ATR depletion, but not ATM, abolished RPA1 depletion-induced FANCD2-Ub, suggesting that ATR activation mediated FANCD2-Ub. Interestingly, we found that depletion of hSSB1/2-INTS3, a single-stranded DNA-binding protein complex, induces FANCD2-Ub, like RPA1 depletion. More interestingly, depletion of either RPA1 or INTS3 caused increased accumulation of DNA damage in FA pathway deficient cell lines. Taken together, these results indicate that RPA deficiency induces activation of the FA pathway in an ATR-dependent manner, which may play a role in the genome maintenance.

  18. Security enhancement of double random phase encoding using rear-mounted phase masking

    Science.gov (United States)

    Chen, Junxin; Zhang, Yu; Li, Jinchang; Zhang, Li-bo

    2018-02-01

    In this paper, a security enhancement for double random phase encoding (DRPE) by introducing a rear-mounted phase masking procedure is presented. Based on exhaustively studying the cryptanalysis achievements of DRPE and its variants, invalidation of the second lens, which plays a critical role in cryptanalyzing processes, is concluded. The improved system can exploit the security potential of the second lens and consequently strengthen the security of DRPE. Experimental results and security analyses are presented in detail to demonstrate the security potential of the proposed cryptosystem.

  19. Mathematic model analysis of Gaussian beam propagation through an arbitrary thickness random phase screen.

    Science.gov (United States)

    Tian, Yuzhen; Guo, Jin; Wang, Rui; Wang, Tingfeng

    2011-09-12

    In order to research the statistical properties of Gaussian beam propagation through an arbitrary thickness random phase screen for adaptive optics and laser communication application in the laboratory, we establish mathematic models of statistical quantities, which are based on the Rytov method and the thin phase screen model, involved in the propagation process. And the analytic results are developed for an arbitrary thickness phase screen based on the Kolmogorov power spectrum. The comparison between the arbitrary thickness phase screen and the thin phase screen shows that it is more suitable for our results to describe the generalized case, especially the scintillation index.

  20. Information hiding based on double random-phase encoding and public-key cryptography.

    Science.gov (United States)

    Sheng, Yuan; Xin, Zhou; Alam, Mohammed S; Xi, Lu; Xiao-Feng, Li

    2009-03-02

    A novel information hiding method based on double random-phase encoding (DRPE) and Rivest-Shamir-Adleman (RSA) public-key cryptosystem is proposed. In the proposed technique, the inherent diffusion property of DRPE is cleverly utilized to make up the diffusion insufficiency of RSA public-key cryptography, while the RSA cryptosystem is utilized for simultaneous transmission of the cipher text and the two phase-masks, which is not possible under the DRPE technique. This technique combines the complementary advantages of the DPRE and RSA encryption techniques and brings security and convenience for efficient information transmission. Extensive numerical simulation results are presented to verify the performance of the proposed technique.

  1. Enhanced wavefront reconstruction by random phase modulation with a phase diffuser

    DEFF Research Database (Denmark)

    Almoro, Percival F; Pedrini, Giancarlo; Gundu, Phanindra Narayan

    2011-01-01

    propagation in free space. The presentation of this technique is carried out using two setups. In the first setup, a diffuser plate is placed at the image plane of a metallic test object. The benefit of randomizing the phase of the object wave is the enhanced intensity recording due to high dynamic range...... of the diffusely scattered beam. The use of demagnification optics will also allow the investigations of relatively large objects. In the second setup, a transparent object is illuminated using a wavefront with random phase and constant amplitude by positioning the phase diffuser close to the object. The benefit...

  2. Efficient Text Encryption and Hiding with Double-Random Phase-Encoding

    Directory of Open Access Journals (Sweden)

    Mohammad S. Alam

    2012-10-01

    Full Text Available In this paper, a double-random phase-encoding technique-based text encryption and hiding method is proposed. First, the secret text is transformed into a 2-dimensional array and the higher bits of the elements in the transformed array are used to store the bit stream of the secret text, while the lower bits are filled with specific values. Then, the transformed array is encoded with double-random phase-encoding technique. Finally, the encoded array is superimposed on an expanded host image to obtain the image embedded with hidden data. The performance of the proposed technique, including the hiding capacity, the recovery accuracy of the secret text, and the quality of the image embedded with hidden data, is tested via analytical modeling and test data stream. Experimental results show that the secret text can be recovered either accurately or almost accurately, while maintaining the quality of the host image embedded with hidden data by properly selecting the method of transforming the secret text into an array and the superimposition coefficient. By using optical information processing techniques, the proposed method has been found to significantly improve the security of text information transmission, while ensuring hiding capacity at a prescribed level.

  3. A random phased array device for delivery of high intensity focused ultrasound

    International Nuclear Information System (INIS)

    Hand, J W; Shaw, A; Sadhoo, N; Rajagopal, S; Dickinson, R J; Gavrilov, L R

    2009-01-01

    Randomized phased arrays can offer electronic steering of a single focus and simultaneous multiple foci concomitant with low levels of secondary maxima and are potentially useful as sources of high intensity focused ultrasound (HIFU). This work describes laboratory testing of a 1 MHz random phased array consisting of 254 elements on a spherical shell of radius of curvature 130 mm and diameter 170 mm. Acoustic output power and efficiency are measured for a range of input electrical powers, and field distributions for various single- and multiple-focus conditions are evaluated by a novel technique using an infrared camera to provide rapid imaging of temperature changes on the surface of an absorbing target. Experimental results show that the array can steer a single focus laterally to at least ±15 mm off axis and axially to more than ±15 mm from the centre of curvature of the array and patterns of four and five simultaneous foci ±10 mm laterally and axially whilst maintaining low intensity levels in secondary maxima away from the targeted area in good agreement with linear theoretical predictions. Experiments in which pork meat was thermally ablated indicate that contiguous lesions several cm 3 in volume can be produced using the patterns of multiple foci.

  4. A random phased array device for delivery of high intensity focused ultrasound.

    Science.gov (United States)

    Hand, J W; Shaw, A; Sadhoo, N; Rajagopal, S; Dickinson, R J; Gavrilov, L R

    2009-10-07

    Randomized phased arrays can offer electronic steering of a single focus and simultaneous multiple foci concomitant with low levels of secondary maxima and are potentially useful as sources of high intensity focused ultrasound (HIFU). This work describes laboratory testing of a 1 MHz random phased array consisting of 254 elements on a spherical shell of radius of curvature 130 mm and diameter 170 mm. Acoustic output power and efficiency are measured for a range of input electrical powers, and field distributions for various single- and multiple-focus conditions are evaluated by a novel technique using an infrared camera to provide rapid imaging of temperature changes on the surface of an absorbing target. Experimental results show that the array can steer a single focus laterally to at least +/-15 mm off axis and axially to more than +/-15 mm from the centre of curvature of the array and patterns of four and five simultaneous foci +/-10 mm laterally and axially whilst maintaining low intensity levels in secondary maxima away from the targeted area in good agreement with linear theoretical predictions. Experiments in which pork meat was thermally ablated indicate that contiguous lesions several cm(3) in volume can be produced using the patterns of multiple foci.

  5. Phosphorylation and cellular function of the human Rpa2 N-terminus in the budding yeast Saccharomyces cerevisiae.

    Science.gov (United States)

    Ghospurkar, Padmaja L; Wilson, Timothy M; Liu, Shengqin; Herauf, Anna; Steffes, Jenna; Mueller, Erica N; Oakley, Gregory G; Haring, Stuart J

    2015-02-01

    Maintenance of genome integrity is critical for proper cell growth. This occurs through accurate DNA replication and repair of DNA lesions. A key factor involved in both DNA replication and the DNA damage response is the heterotrimeric single-stranded DNA (ssDNA) binding complex Replication Protein A (RPA). Although the RPA complex appears to be structurally conserved throughout eukaryotes, the primary amino acid sequence of each subunit can vary considerably. Examination of sequence differences along with the functional interchangeability of orthologous RPA subunits or regions could provide insight into important regions and their functions. This might also allow for study in simpler systems. We determined that substitution of yeast Replication Factor A (RFA) with human RPA does not support yeast cell viability. Exchange of a single yeast RFA subunit with the corresponding human RPA subunit does not function due to lack of inter-species subunit interactions. Substitution of yeast Rfa2 with domains/regions of human Rpa2 important for Rpa2 function (i.e., the N-terminus and the loop 3-4 region) supports viability in yeast cells, and hybrid proteins containing human Rpa2 N-terminal phospho-mutations result in similar DNA damage phenotypes to analogous yeast Rfa2 N-terminal phospho-mutants. Finally, the human Rpa2 N-terminus (NT) fused to yeast Rfa2 is phosphorylated in a manner similar to human Rpa2 in human cells, indicating that conserved kinases recognize the human domain in yeast. The implication is that budding yeast represents a potential model system for studying not only human Rpa2 N-terminal phosphorylation, but also phosphorylation of Rpa2 N-termini from other eukaryotic organisms. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  6. Conserving RPA and the response of 48Ca

    International Nuclear Information System (INIS)

    Brand, M.G.E.; Allaart, K.; Dickhoff, W.H.

    1988-01-01

    The connection between the single-particle self-energy and the corresponding conserving particle-hole (ph) interaction, discussed long ago by Kadanoff and Baym, is employed to study the response of 48 Ca. Second order self-energy contributions are taken into account in the construction of the energy dependent ph interaction. From this perspective it is possible to make contact with other approaches which also aim to incorporate the coupling to 2p2h excitations within the RPA framework. The method is used to study both the discrete low-energy states as well as the giant resonances in both 48 Ca and 48 Sc using a realistic G matrix interaction based on meson exchange. The calculated strength distribution compares favorably with experimental but the strength below 15 MeV is still somewhat too large as compared to experiment for all types of excitations. The quenching of magnetic and Gamow-Teller strength due to 2p2h admixture amounts to about 30%. (orig.)

  7. High-affinity DNA-binding Domains of Replication Protein A (RPA) Direct SMARCAL1-dependent Replication Fork Remodeling*

    Science.gov (United States)

    Bhat, Kamakoti P.; Bétous, Rémy; Cortez, David

    2015-01-01

    SMARCAL1 catalyzes replication fork remodeling to maintain genome stability. It is recruited to replication forks via an interaction with replication protein A (RPA), the major ssDNA-binding protein in eukaryotic cells. In addition to directing its localization, RPA also activates SMARCAL1 on some fork substrates but inhibits it on others, thereby conferring substrate specificity to SMARCAL1 fork-remodeling reactions. We investigated the mechanism by which RPA regulates SMARCAL1. Our results indicate that although an interaction between SMARCAL1 and RPA is essential for SMARCAL1 activation, the location of the interacting surface on RPA is not. Counterintuitively, high-affinity DNA binding of RPA DNA-binding domain (DBD) A and DBD-B near the fork junction makes it easier for SMARCAL1 to remodel the fork, which requires removing RPA. We also found that RPA DBD-C and DBD-D are not required for SMARCAL1 regulation. Thus, the orientation of the high-affinity RPA DBDs at forks dictates SMARCAL1 substrate specificity. PMID:25552480

  8. High-affinity DNA-binding domains of replication protein A (RPA) direct SMARCAL1-dependent replication fork remodeling.

    Science.gov (United States)

    Bhat, Kamakoti P; Bétous, Rémy; Cortez, David

    2015-02-13

    SMARCAL1 catalyzes replication fork remodeling to maintain genome stability. It is recruited to replication forks via an interaction with replication protein A (RPA), the major ssDNA-binding protein in eukaryotic cells. In addition to directing its localization, RPA also activates SMARCAL1 on some fork substrates but inhibits it on others, thereby conferring substrate specificity to SMARCAL1 fork-remodeling reactions. We investigated the mechanism by which RPA regulates SMARCAL1. Our results indicate that although an interaction between SMARCAL1 and RPA is essential for SMARCAL1 activation, the location of the interacting surface on RPA is not. Counterintuitively, high-affinity DNA binding of RPA DNA-binding domain (DBD) A and DBD-B near the fork junction makes it easier for SMARCAL1 to remodel the fork, which requires removing RPA. We also found that RPA DBD-C and DBD-D are not required for SMARCAL1 regulation. Thus, the orientation of the high-affinity RPA DBDs at forks dictates SMARCAL1 substrate specificity. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  9. A DNA Barcode-Based RPA Assay (BAR-RPA) for Rapid Identification of the Dry Root of Ficus hirta (Wuzhimaotao).

    Science.gov (United States)

    Tian, Enwei; Liu, Qianqian; Ye, Haoting; Li, Fang; Chao, Zhi

    2017-12-18

    Background: Wuzhimaotao (the dry root of Ficus hirta ) is used as both medicine and food ingredient by the locals in areas around Nanling Mountains of China. Due to its very similar external morphologies with Duanchangcao (the root of Gelsemium elegans , which contains gelsemine that is extremely neurotoxic) and the associated growth of these two plants, incidents of food poisoning and even death frequently occur, resulting from the misuse of Duanchangcao as Wuzhimaotao. The aim of this study is to develop a fast, even, on-spot approach to identification of Wuzhimaotao. Methods: We used DNA barcode-based recombinase polymerase amplification (BAR-RPA) with species-specific primers targeting the internal transcribed spacer (ITS) region of the rDNA of F. hirta. BAR-RPA reaction time and temperature were optimized and the specificity and sensitivity of BAR-RPA species-specific primers were assessed. Results: This technique showed a high specificity and sensitivity to amplify the genomic DNA of F. hirta and allowed for rapid amplification (within 15 min) of the ITS region under a constant and mild temperature range of 37-42 °C without using thermocyclers. Conclusions: The BAR-RPA assay with a fast DNA extraction protocol provides a simple, energy-saving, and rapid method for identification of Wuzhimaotao in both laboratory and field settings.

  10. A DNA Barcode-Based RPA Assay (BAR-RPA for Rapid Identification of the Dry Root of Ficus hirta (Wuzhimaotao

    Directory of Open Access Journals (Sweden)

    Enwei Tian

    2017-12-01

    Full Text Available Background: Wuzhimaotao (the dry root of Ficus hirta is used as both medicine and food ingredient by the locals in areas around Nanling Mountains of China. Due to its very similar external morphologies with Duanchangcao (the root of Gelsemium elegans, which contains gelsemine that is extremely neurotoxic and the associated growth of these two plants, incidents of food poisoning and even death frequently occur, resulting from the misuse of Duanchangcao as Wuzhimaotao. The aim of this study is to develop a fast, even, on-spot approach to identification of Wuzhimaotao. Methods: We used DNA barcode-based recombinase polymerase amplification (BAR-RPA with species–specific primers targeting the internal transcribed spacer (ITS region of the rDNA of F. hirta. BAR-RPA reaction time and temperature were optimized and the specificity and sensitivity of BAR-RPA species–specific primers were assessed. Results: This technique showed a high specificity and sensitivity to amplify the genomic DNA of F. hirta and allowed for rapid amplification (within 15 min of the ITS region under a constant and mild temperature range of 37–42 °C without using thermocyclers. Conclusions: The BAR-RPA assay with a fast DNA extraction protocol provides a simple, energy-saving, and rapid method for identification of Wuzhimaotao in both laboratory and field settings.

  11. RPA facilitates telomerase activity at chromosome ends in budding and fission yeasts.

    Science.gov (United States)

    Luciano, Pierre; Coulon, Stéphane; Faure, Virginie; Corda, Yves; Bos, Julia; Brill, Steven J; Gilson, Eric; Simon, Marie-Noelle; Géli, Vincent

    2012-04-18

    In Saccharomyces cerevisiae, the telomerase complex binds to chromosome ends and is activated in late S-phase through a process coupled to the progression of the replication fork. Here, we show that the single-stranded DNA-binding protein RPA (replication protein A) binds to the two daughter telomeres during telomere replication but only its binding to the leading-strand telomere depends on the Mre11/Rad50/Xrs2 (MRX) complex. We further demonstrate that RPA specifically co-precipitates with yKu, Cdc13 and telomerase. The interaction of RPA with telomerase appears to be mediated by both yKu and the telomerase subunit Est1. Moreover, a mutation in Rfa1 that affects both the interaction with yKu and telomerase reduces the dramatic increase in telomere length of a rif1Δ, rif2Δ double mutant. Finally, we show that the RPA/telomerase association and function are conserved in Schizosaccharomyces pombe. Our results indicate that in both yeasts, RPA directly facilitates telomerase activity at chromosome ends.

  12. G9a coordinates with the RPA complex to promote DNA damage repair and cell survival.

    Science.gov (United States)

    Yang, Qiaoyan; Zhu, Qian; Lu, Xiaopeng; Du, Yipeng; Cao, Linlin; Shen, Changchun; Hou, Tianyun; Li, Meiting; Li, Zhiming; Liu, Chaohua; Wu, Di; Xu, Xingzhi; Wang, Lina; Wang, Haiying; Zhao, Ying; Yang, Yang; Zhu, Wei-Guo

    2017-07-25

    Histone methyltransferase G9a has critical roles in promoting cancer-cell growth and gene suppression, but whether it is also associated with the DNA damage response is rarely studied. Here, we report that loss of G9a impairs DNA damage repair and enhances the sensitivity of cancer cells to radiation and chemotherapeutics. In response to DNA double-strand breaks (DSBs), G9a is phosphorylated at serine 211 by casein kinase 2 (CK2) and recruited to chromatin. The chromatin-enriched G9a can then directly interact with replication protein A (RPA) and promote loading of the RPA and Rad51 recombinase to DSBs. This mechanism facilitates homologous recombination (HR) and cell survival. We confirmed the interaction between RPA and G9a to be critical for RPA foci formation and HR upon DNA damage. Collectively, our findings demonstrate a regulatory pathway based on CK2-G9a-RPA that permits HR in cancer cells and provide further rationale for the use of G9a inhibitors as a cancer therapeutic.

  13. Viral interference with DNA repair by targeting of the single-stranded DNA binding protein RPA.

    Science.gov (United States)

    Banerjee, Pubali; DeJesus, Rowena; Gjoerup, Ole; Schaffhausen, Brian S

    2013-10-01

    Correct repair of damaged DNA is critical for genomic integrity. Deficiencies in DNA repair are linked with human cancer. Here we report a novel mechanism by which a virus manipulates DNA damage responses. Infection with murine polyomavirus sensitizes cells to DNA damage by UV and etoposide. Polyomavirus large T antigen (LT) alone is sufficient to sensitize cells 100 fold to UV and other kinds of DNA damage. This results in activated stress responses and apoptosis. Genetic analysis shows that LT sensitizes via the binding of its origin-binding domain (OBD) to the single-stranded DNA binding protein replication protein A (RPA). Overexpression of RPA protects cells expressing OBD from damage, and knockdown of RPA mimics the LT phenotype. LT prevents recruitment of RPA to nuclear foci after DNA damage. This leads to failure to recruit repair proteins such as Rad51 or Rad9, explaining why LT prevents repair of double strand DNA breaks by homologous recombination. A targeted intervention directed at RPA based on this viral mechanism could be useful in circumventing the resistance of cancer cells to therapy.

  14. Analysis of double random phase encryption from a key-space perspective

    Science.gov (United States)

    Monaghan, David S.; Situ, Guohai; Ryle, James; Gopinathan, Unnikrishnan; Naughton, Thomas J.; Sheridan, John T.

    2007-09-01

    The main advantage of the double random phase encryption technique is its physical implementation however to allow us to analyse its behaviour we perform the encryption/decryption numerically. A typically strong encryption scheme will have an extremely large key-space, which will make the probable success of any brute force attack on that algorithm miniscule. Traditionally, designers of optical image encryption systems only demonstrate how a small number of arbitrary keys cannot decrypt a chosen encrypted image in their system. We analyse this algorithm from a key-space perspective. The key-space of an encryption algorithm can be defined as the set of possible keys that can be used to encode data using that algorithm. For a range of problem instances we plot the distribution of decryption errors in the key-space indicating the lack of feasibility of a simple brute force attack.

  15. Random phase plate hot spots and their effect on stimulated Brillouin backscatter and self-focusing

    International Nuclear Information System (INIS)

    Rose, H.A.

    1995-01-01

    Laser hot spots, as determined by Random Phase Plate (RPP) hot spots, control the critical value of the average intensity, I c , at which there is a rapid onset of stimulated scatter in the strongly damped convective regime of three wave parametric instabilities. For the case of stimulated Brillouin backscatter in a long scale length plasma, nascent hot spot ponderomotive self-focusing is shown to reduce the value of I c in the regime of very strongly damped acoustic waves. RPP hot spots have two, intrinsically nonlinear, thresholds for ponderomotive self-focusing. Large intensity amplifications occur in the hot spot neighborhood when the hot spot power exceeds a certain critical power, P c , which is independent of the optic's f number, F. When the second, F-dependent, hot spot power threshold is exceeded, a filament emerges from the far side of the hot spot, whose extent grows erratically in time

  16. Statistical properties of laser hot spots produced by a random phase plate

    International Nuclear Information System (INIS)

    Rose, H.A.; DuBois, D.F.

    1993-01-01

    A quantitative theory of laser hot spots, which control plasma instabilities in real laser--plasma interactions, is presented in the case of random phase plate (RPP) optics. It is shown that the probability density of intense hot spots with intensity I, P hot (I), is given by P hot (I)∼(I/I 0 2 )exp(-I/I 0 ) where I 0 is the average intensity, and that the detailed amplitude and phase variation of the laser field in the vicinity of an intense hot spot is uniquely specified by the optics and is deterministic. These hot spots may be the source of below threshold stimulated Raman scattering (SRS) and its variation with I 0 is shown to be super exponential. A brief preview of a quantitative nonlinear theory of hot-spot-induced laser filamentation is presented

  17. Disorder Induced Dynamic Equilibrium Localization and Random Phase Steps of Bose—Einstein Condensates

    International Nuclear Information System (INIS)

    Duan Ya-Fan; Xu Zhen; Qian Jun; Sun Jian-Fang; Jiang Bo-Nan; Hong Tao

    2011-01-01

    We numerically analyze the dynamic behavior of Bose—Einstein condensate (BEC) in a one-dimensional disordered potential before it completely loses spatial quantum coherence. We find that both the disorder statistics and the atom interactions produce remarkable effects on localization. We also find that the single phase of the initial condensate is broken into many small pieces while the system approaches localization, showing a counter-intuitive step-wise phase but not a thoroughly randomized phase. Although the condensates as a whole show less flow and expansion, the currents between adjacent phase steps retain strong time dependence. Thus we show explicitly that the localization of a finite size Bose—Einstein condensate is a dynamic equilibrium state. (general)

  18. Encoding plaintext by Fourier transform hologram in double random phase encoding using fingerprint keys

    Science.gov (United States)

    Takeda, Masafumi; Nakano, Kazuya; Suzuki, Hiroyuki; Yamaguchi, Masahiro

    2012-09-01

    It has been shown that biometric information can be used as a cipher key for binary data encryption by applying double random phase encoding. In such methods, binary data are encoded in a bit pattern image, and the decrypted image becomes a plain image when the key is genuine; otherwise, decrypted images become random images. In some cases, images decrypted by imposters may not be fully random, such that the blurred bit pattern can be partially observed. In this paper, we propose a novel bit coding method based on a Fourier transform hologram, which makes images decrypted by imposters more random. Computer experiments confirm that the method increases the randomness of images decrypted by imposters while keeping the false rejection rate as low as in the conventional method.

  19. Encoding plaintext by Fourier transform hologram in double random phase encoding using fingerprint keys

    International Nuclear Information System (INIS)

    Takeda, Masafumi; Nakano, Kazuya; Suzuki, Hiroyuki; Yamaguchi, Masahiro

    2012-01-01

    It has been shown that biometric information can be used as a cipher key for binary data encryption by applying double random phase encoding. In such methods, binary data are encoded in a bit pattern image, and the decrypted image becomes a plain image when the key is genuine; otherwise, decrypted images become random images. In some cases, images decrypted by imposters may not be fully random, such that the blurred bit pattern can be partially observed. In this paper, we propose a novel bit coding method based on a Fourier transform hologram, which makes images decrypted by imposters more random. Computer experiments confirm that the method increases the randomness of images decrypted by imposters while keeping the false rejection rate as low as in the conventional method. (paper)

  20. RPA-Binding Protein ETAA1 Is an ATR Activator Involved in DNA Replication Stress Response.

    Science.gov (United States)

    Lee, Yuan-Cho; Zhou, Qing; Chen, Junjie; Yuan, Jingsong

    2016-12-19

    ETAA1 (Ewing tumor-associated antigen 1), also known as ETAA16, was identified as a tumor-specific antigen in the Ewing family of tumors. However, the biological function of this protein remains unknown. Here, we report the identification of ETAA1 as a DNA replication stress response protein. ETAA1 specifically interacts with RPA (Replication protein A) via two conserved RPA-binding domains and is therefore recruited to stalled replication forks. Interestingly, further analysis of ETAA1 function revealed that ETAA1 participates in the activation of ATR signaling pathway via a conserved ATR-activating domain (AAD) located near its N terminus. Importantly, we demonstrate that both RPA binding and ATR activation are required for ETAA1 function at stalled replication forks to maintain genome stability. Therefore, our data suggest that ETAA1 is a new ATR activator involved in replication checkpoint control. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. RPA-coated single-stranded DNA as a platform for post-translational modifications in the DNA damage response.

    Science.gov (United States)

    Maréchal, Alexandre; Zou, Lee

    2015-01-01

    The Replication Protein A (RPA) complex is an essential regulator of eukaryotic DNA metabolism. RPA avidly binds to single-stranded DNA (ssDNA) through multiple oligonucleotide/oligosaccharide-binding folds and coordinates the recruitment and exchange of genome maintenance factors to regulate DNA replication, recombination and repair. The RPA-ssDNA platform also constitutes a key physiological signal which activates the master ATR kinase to protect and repair stalled or collapsed replication forks during replication stress. In recent years, the RPA complex has emerged as a key target and an important regulator of post-translational modifications in response to DNA damage, which is critical for its genome guardian functions. Phosphorylation and SUMOylation of the RPA complex, and more recently RPA-regulated ubiquitination, have all been shown to control specific aspects of DNA damage signaling and repair by modulating the interactions between RPA and its partners. Here, we review our current understanding of the critical functions of the RPA-ssDNA platform in the maintenance of genome stability and its regulation through an elaborate network of covalent modifications.

  2. RpA, an extracellular protease similar to the metalloprotease of serralysin family, is required for pathogenicity of Ralstonia pickettii.

    Science.gov (United States)

    Chen, C-M; Liu, J-J; Chou, C-W; Lai, C-H; Wu, L-T

    2015-10-01

    To investigate the biochemical and functional properties of an extracellular protease, RpA, in Ralstonia pickettii WP1 isolated from water supply systems. An extracellular protease was identified and characterized from R. pickettii WP1. A mutant strain WP1M2 was created from strain WP1 by mini-Tn5 transposition. The culture filtrates from WP1M2 had a lower cytotoxic effect than the parental WP1 on several mammalian cell lines. Cloning and sequence analysis revealed the Tn5 transposon inserted at a protease gene (rpA) which is 81% homologous to prtA and aprX genes of Pseudomonas fluorescens. The rpA gene encodes a 482-residue protein showing sequence similarity to metalloproteases of the serralysin family. The RpA protein was expressed in Escherichia coli using a pET expression vector and purified as a 55 kDa molecular weight protein. Furthermore, the protease activity of RpA was inhibited by protease inhibitor and heat treatment. The in vitro cytotoxic activity of R. pickettii culture filtrates was attributed to RpA protease. An extracellular protease, RpA, was identified from R. pickettii WP1 isolated from water supply system. The RpA metalloproteases is required for the pathogenicity of R. pickettii to mammalian cell lines. © 2015 The Society for Applied Microbiology.

  3. DNA-PK, ATM and ATR collaboratively regulate p53-RPA interaction to facilitate homologous recombination DNA repair.

    Science.gov (United States)

    Serrano, M A; Li, Z; Dangeti, M; Musich, P R; Patrick, S; Roginskaya, M; Cartwright, B; Zou, Y

    2013-05-09

    Homologous recombination (HR) and nonhomologous end joining (NHEJ) are two distinct DNA double-stranded break (DSB) repair pathways. Here, we report that DNA-dependent protein kinase (DNA-PK), the core component of NHEJ, partnering with DNA-damage checkpoint kinases ataxia telangiectasia mutated (ATM) and ATM- and Rad3-related (ATR), regulates HR repair of DSBs. The regulation was accomplished through modulation of the p53 and replication protein A (RPA) interaction. We show that upon DNA damage, p53 and RPA were freed from a p53-RPA complex by simultaneous phosphorylations of RPA at the N-terminus of RPA32 subunit by DNA-PK and of p53 at Ser37 and Ser46 in a Chk1/Chk2-independent manner by ATR and ATM, respectively. Neither the phosphorylation of RPA nor of p53 alone could dissociate p53 and RPA. Furthermore, disruption of the release significantly compromised HR repair of DSBs. Our results reveal a mechanism for the crosstalk between HR repair and NHEJ through the co-regulation of p53-RPA interaction by DNA-PK, ATM and ATR.

  4. Development and Evaluation of a Rapid and Sensitive EBOV-RPA Test for Rapid Diagnosis of Ebola Virus Disease.

    Science.gov (United States)

    Yang, Mingjuan; Ke, Yuehua; Wang, Xuesong; Ren, Hang; Liu, Wei; Lu, Huijun; Zhang, Wenyi; Liu, Shiwei; Chang, Guohui; Tian, Shuguang; Wang, Lihua; Huang, Liuyu; Liu, Chao; Yang, Ruifu; Chen, Zeliang

    2016-06-01

    Confirming Ebola virus disease (EVD), a deadly infectious disease, requires real-time RT-PCR, which takes up to a few hours to yield results. Therefore, a rapid diagnostic assay is imperative for EVD diagnosis. A rapid nucleic acid test based on recombinase polymerase amplification (EBOV-RPA) was developed to specifically detect the 2014 outbreak strains. The EBOV-RPA assay was evaluated by testing samples from suspected EVD patients in parallel with RT-PCR. An EBOV-RPA, which could be completed in 20 min, was successfully developed. Of 271 patients who tested positive for Ebola virus by RT-PCR, 264 (sensitivity: 97%, 95% CI: 95.5-99.3%) were positive by EBOV-RPA; 101 of 104 patients (specificity: 97%, 95% CI: 93.9-100%) who tested negative by RT-PCR were also negative by EBOV-RPA. The sensitivity values for samples with a Ct value of RPA had significantly high Ct values. Results of external quality assessment samples with EBOV-RPA were 100%, consistent with those of RT-PCR. The EBOV-RPA assay showed 97% sensitivity and 97% specificity for all EVD samples tested, making it a rapid and sensitive test for EVD diagnosis.

  5. 78 FR 8511 - RPA Energy, Inc.; Supplemental Notice That Initial Market-Based Rate Filing Includes Request for...

    Science.gov (United States)

    2013-02-06

    ... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission [Docket No. ER13-826-000] RPA Energy, Inc.; Supplemental Notice That Initial Market-Based Rate Filing Includes Request for Blanket Section 204 Authorization This is a supplemental notice in the above-referenced proceeding, of RPA Energy, Inc...

  6. Differences in immunolocalization of Kim-1, RPA-1, and RPA-2 in kidneys of gentamicin-, cisplatin-, and valproic acid-treated rats: potential role of iNOS and nitrotyrosine.

    Science.gov (United States)

    Zhang, Jun; Goering, Peter L; Espandiari, Parvaneh; Shaw, Martin; Bonventre, Joseph V; Vaidya, Vishal S; Brown, Ronald P; Keenan, Joe; Kilty, Cormac G; Sadrieh, Nakissa; Hanig, Joseph P

    2009-08-01

    The present study compared the immunolocalization of Kim-1, renal papillary antigen (RPA)-1, and RPA-2 with that of inducible nitric oxide synthase (iNOS) and nitrotyrosine in kidneys of gentamicin sulfate (Gen)- and cisplatin (Cis)-treated rats. The specificity of acute kidney injury (AKI) biomarkers, iNOS, and nitrotyrosine was evaluated by dosing rats with valproic acid (VPA). Sprague-Dawley (SD) rats were injected subcutaneously (sc) with 100 mg/kg/day of Gen for six or fourteen days; a single intraperitoneal (ip) dose of 1, 3, or 6 mg/kg of Cis; or 650 mg/kg/day of VPA (ip) for four days. In Gen-treated rats, Kim-1 was expressed in the epithelial cells, mainly in the S1/S2 segments but less so in the S3 segment, and RPA-1 was increased in the epithelial cells of collecting ducts (CD) in the cortex. Spatial expression of iNOS or nitrotyrosine with Kim-1 or RPA-1 was detected. In Cis-treated rats, Kim-1 was expressed only in the S3 segment cells, and RPA-1 and RPA-2 were increased in the epithelial cells of medullary CD or medullary loop of Henle (LH), respectively. Spatial expression of iNOS or nitrotyrosine with RPA-1 or RPA-2 was also identified. These findings suggest that peroxynitrite formation may be involved in the pathogenesis of Gen and Cis nephrotoxicity and that Kim-1, RPA-1, and RPA-2 have the potential to serve as site-specific biomarkers for Gen or Cis AKI.

  7. Dpb11 may function with RPA and DNA to initiate DNA replication.

    Science.gov (United States)

    Bruck, Irina; Dhingra, Nalini; Martinez, Matthew P; Kaplan, Daniel L

    2017-01-01

    Dpb11 is required for the initiation of DNA replication in budding yeast. We found that Dpb11 binds tightly to single-stranded DNA (ssDNA) or branched DNA structures, while its human homolog, TopBP1, binds tightly to branched-DNA structures. We also found that Dpb11 binds stably to CDK-phosphorylated RPA, the eukaryotic ssDNA binding protein, in the presence of branched DNA. A Dpb11 mutant specifically defective for DNA binding did not exhibit tight binding to RPA in the presence of DNA, suggesting that Dpb11-interaction with DNA may promote the recruitment of RPA to melted DNA. We then characterized a mutant of Dpb11 that is specifically defective in DNA binding in budding yeast cells. Expression of dpb11-m1,2,3,5,ΔC results in a substantial decrease in RPA recruitment to origins, suggesting that Dpb11 interaction with DNA may be required for RPA recruitment to origins. Expression of dpb11-m1,2,3,5,ΔC also results in diminished GINS interaction with Mcm2-7 during S phase, while Cdc45 interaction with Mcm2-7 is like wild-type. The reduced GINS interaction with Mcm2-7 may be an indirect consequence of diminished origin melting. We propose that the tight interaction between Dpb11, CDK-phosphorylated RPA, and branched-DNA may be required for the essential function of stabilizing melted origin DNA in vivo. We also propose an alternative model, wherein Dpb11-DNA interaction is required for some other function in DNA replication initiation, such as helicase activation.

  8. The second RPA description for the decay of the one-phonon nuclear collective states at finite temperature

    International Nuclear Information System (INIS)

    Yannouleas, C.; Jang, S.

    1986-01-01

    The zero-temperature second RPA is generalized to finite temperatures through the use of the method of linearization of the equations of motion. After elimination of the quadruples, for low enough temperatures and within the subspace spanned by the doubles, a proper symmetrization yields an eigenvalue equation which exhibits formal properties like the simple RPA. From this second RPA eigenvalue equation, a closed formula for the spreading width of an isolated collective state is extracted. The second RPA can be recast in the form of a generalized collision term and be compared with the method of the Bethe-Salpeter equation for the two-body Green function. However, the second RPA method (and results) contrasts with the approach (and corresponding results) of the Boltzmann collision term, which is usually viewed as the appropriate agent for nuclear dissipation. (orig.)

  9. Cell cycle-specific UNG2 phosphorylations regulate protein turnover, activity and association with RPA

    DEFF Research Database (Denmark)

    Hagen, Lars; Kavli, Bodil; Sousa, Mirta M L

    2008-01-01

    -catalytic domain that confer distinct functional properties to UNG2. These are apparently generated by cyclin-dependent kinases through stepwise phosphorylation of S23, T60 and S64 in the cell cycle. Phosphorylation of S23 in late G1/early S confers increased association with replication protein A (RPA......) and replicating chromatin and markedly increases the catalytic turnover of UNG2. Conversely, progressive phosphorylation of T60 and S64 throughout S phase mediates reduced binding to RPA and flag UNG2 for breakdown in G2 by forming a cyclin E/c-myc-like phosphodegron. The enhanced catalytic turnover of UNG2 p-S23...

  10. Activation of the ATR kinase by the RPA-binding protein ETAA1

    DEFF Research Database (Denmark)

    Haahr, Peter; Hoffmann, Saskia; Tollenaere, Maxim A X

    2016-01-01

    Activation of the ATR kinase following perturbations to DNA replication relies on a complex mechanism involving ATR recruitment to RPA-coated single-stranded DNA via its binding partner ATRIP and stimulation of ATR kinase activity by TopBP1. Here, we discovered an independent ATR activation pathway...... in vertebrates, mediated by the uncharacterized protein ETAA1 (Ewing's tumour-associated antigen 1). Human ETAA1 accumulates at DNA damage sites via dual RPA-binding motifs and promotes replication fork progression and integrity, ATR signalling and cell survival after genotoxic insults. Mechanistically...

  11. Diophantine approximation and badly approximable sets

    DEFF Research Database (Denmark)

    Kristensen, S.; Thorn, R.; Velani, S.

    2006-01-01

    . The classical set Bad of `badly approximable' numbers in the theory of Diophantine approximation falls within our framework as do the sets Bad(i,j) of simultaneously badly approximable numbers. Under various natural conditions we prove that the badly approximable subsets of Omega have full Hausdorff dimension...

  12. Nonclassical effects in plasmonics: an energy perspective to quantify nonclassical effects

    DEFF Research Database (Denmark)

    Yan, Wei; Mortensen, N. Asger

    2016-01-01

    of the nonclassical effects at different microscopic levels by contrasting the numerical results from the semiclassical hydrodynamic Drude model (HDM) and the microscopic random-phase approximation (RPA). The formal relation between the HDM and the RPA is also established for metals by exploring the limit...

  13. Adiabatic-connection fluctuation-dissipation DFT for the structural properties of solids - The renormalized ALDA and electron gas kernels

    DEFF Research Database (Denmark)

    Patrick, Christopher E.; Thygesen, Kristian Sommer

    2015-01-01

    the atomization energy of the H2 molecule. We compare the results calculated with different kernels to those obtained from the random-phase approximation (RPA) and to experimental measurements. We demonstrate that the model kernels correct the RPA's tendency to overestimate the magnitude of the correlation energy...

  14. Spin flipping in ring-coupled-cluster-doubles theory

    DEFF Research Database (Denmark)

    Klopper, Wim; M. Teale, Andrew; Coriani, Sonia

    2011-01-01

    We report a critical analysis and comparison of a variety of random-phase-approximation (RPA) based approaches to determine the electronic ground-state energy. Interrelations between RPA variants are examined by numerical examples with particular attention paid to the role of spin......-flipped excitations and the behaviour of the adiabatic-connection integrands where appropriate. In general, it is found that RPA variants that include Hartree–Fock exchange contributions are unsuitable as generally applicable methods for the determination of correlation energies. Of the remaining methods only...... the direct RPA and RPA with second-order screened exchange are recommended for general use....

  15. Double random phase spread spectrum spread space technique for secure parallel optical multiplexing with individual encryption key

    Science.gov (United States)

    Hennelly, B. M.; Javidi, B.; Sheridan, J. T.

    2005-09-01

    A number of methods have been recently proposed in the literature for the encryption of 2-D information using linear optical systems. In particular the double random phase encoding system has received widespread attention. This system uses two Random Phase Keys (RPK) positioned in the input spatial domain and the spatial frequency domain and if these random phases are described by statistically independent white noises then the encrypted image can be shown to be a white noise. Decryption only requires knowledge of the RPK in the frequency domain. The RPK may be implemented using a Spatial Light Modulators (SLM). In this paper we propose and investigate the use of SLMs for secure optical multiplexing. We show that in this case it is possible to encrypt multiple images in parallel and multiplex them for transmission or storage. The signal energy is effectively spread in the spatial frequency domain. As expected the number of images that can be multiplexed together and recovered without loss is proportional to the ratio of the input image and the SLM resolution. Many more images may be multiplexed with some loss in recovery. Furthermore each individual encryption is more robust than traditional double random phase encoding since decryption requires knowledge of both RPK and a lowpass filter in order to despread the spectrum and decrypt the image. Numerical simulations are presented and discussed.

  16. The use of odd random phase electrochemical impedance spectroscopy to study lithium-based corrosion inhibition by active protective coatings

    NARCIS (Netherlands)

    Meeusen, M.; Visser, P.; Fernández Macía, L.; Hubin, A.; Terryn, H.A.; Mol, J.M.C.

    2018-01-01

    In this work, the study of the time-dependent behaviour of lithium carbonate based inhibitor technology for the active corrosion protection of aluminium alloy 2024-T3 is presented. Odd random phase electrochemical impedance spectroscopy (ORP-EIS) is selected as the electrochemical tool to study

  17. A multispectral photon-counting double random phase encoding scheme for image authentication.

    Science.gov (United States)

    Yi, Faliu; Moon, Inkyu; Lee, Yeon H

    2014-05-20

    In this paper, we propose a new method for color image-based authentication that combines multispectral photon-counting imaging (MPCI) and double random phase encoding (DRPE) schemes. The sparsely distributed information from MPCI and the stationary white noise signal from DRPE make intruder attacks difficult. In this authentication method, the original multispectral RGB color image is down-sampled into a Bayer image. The three types of color samples (red, green and blue color) in the Bayer image are encrypted with DRPE and the amplitude part of the resulting image is photon counted. The corresponding phase information that has nonzero amplitude after photon counting is then kept for decryption. Experimental results show that the retrieved images from the proposed method do not visually resemble their original counterparts. Nevertheless, the original color image can be efficiently verified with statistical nonlinear correlations. Our experimental results also show that different interpolation algorithms applied to Bayer images result in different verification effects for multispectral RGB color images.

  18. Biometrics based key management of double random phase encoding scheme using error control codes

    Science.gov (United States)

    Saini, Nirmala; Sinha, Aloka

    2013-08-01

    In this paper, an optical security system has been proposed in which key of the double random phase encoding technique is linked to the biometrics of the user to make it user specific. The error in recognition due to the biometric variation is corrected by encoding the key using the BCH code. A user specific shuffling key is used to increase the separation between genuine and impostor Hamming distance distribution. This shuffling key is then further secured using the RSA public key encryption to enhance the security of the system. XOR operation is performed between the encoded key and the feature vector obtained from the biometrics. The RSA encoded shuffling key and the data obtained from the XOR operation are stored into a token. The main advantage of the present technique is that the key retrieval is possible only in the simultaneous presence of the token and the biometrics of the user which not only authenticates the presence of the original input but also secures the key of the system. Computational experiments showed the effectiveness of the proposed technique for key retrieval in the decryption process by using the live biometrics of the user.

  19. Steganographic optical image encryption system based on reversible data hiding and double random phase encoding

    Science.gov (United States)

    Chuang, Cheng-Hung; Chen, Yen-Lin

    2013-02-01

    This study presents a steganographic optical image encryption system based on reversible data hiding and double random phase encoding (DRPE) techniques. Conventional optical image encryption systems can securely transmit valuable images using an encryption method for possible application in optical transmission systems. The steganographic optical image encryption system based on the DRPE technique has been investigated to hide secret data in encrypted images. However, the DRPE techniques vulnerable to attacks and many of the data hiding methods in the DRPE system can distort the decrypted images. The proposed system, based on reversible data hiding, uses a JBIG2 compression scheme to achieve lossless decrypted image quality and perform a prior encryption process. Thus, the DRPE technique enables a more secured optical encryption process. The proposed method extracts and compresses the bit planes of the original image using the lossless JBIG2 technique. The secret data are embedded in the remaining storage space. The RSA algorithm can cipher the compressed binary bits and secret data for advanced security. Experimental results show that the proposed system achieves a high data embedding capacity and lossless reconstruction of the original images.

  20. A Multispectral Photon-Counting Double Random Phase Encoding Scheme for Image Authentication

    Directory of Open Access Journals (Sweden)

    Faliu Yi

    2014-05-01

    Full Text Available In this paper, we propose a new method for color image-based authentication that combines multispectral photon-counting imaging (MPCI and double random phase encoding (DRPE schemes. The sparsely distributed information from MPCI and the stationary white noise signal from DRPE make intruder attacks difficult. In this authentication method, the original multispectral RGB color image is down-sampled into a Bayer image. The three types of color samples (red, green and blue color in the Bayer image are encrypted with DRPE and the amplitude part of the resulting image is photon counted. The corresponding phase information that has nonzero amplitude after photon counting is then kept for decryption. Experimental results show that the retrieved images from the proposed method do not visually resemble their original counterparts. Nevertheless, the original color image can be efficiently verified with statistical nonlinear correlations. Our experimental results also show that different interpolation algorithms applied to Bayer images result in different verification effects for multispectral RGB color images.

  1. Particle-particle and hole-hole RPA correlations at finite temperature and the temperature dependence of the level density parameter

    International Nuclear Information System (INIS)

    Vinh Mau, N.

    1987-11-01

    The pp-hh RPA equations obtained by summing the infinite series of ladder, upwards and backwards going diagrams in the temperature two particle Green's functions are derived at finite temperature. The contribution to the thermodynamic grand potential due to pp-hh RPA correlations is calculated simultaneously to that of ph RPA correlations. A schematic model is constructed which shows that, as for ph RPA states, the energies of pp and hh RPA states have no temperature dependence at not too high temperature. Within the same model, the temperature dependence of the level density parameter is discussed

  2. Particle-particle and hole-hole RPA correlations at finite temperature and the temperature dependence of the level density parameter

    International Nuclear Information System (INIS)

    Vinh Mau, N.

    1989-01-01

    The pp-hh RPA equations obtained by summing the infinite series of ladder, upwards- and backwards-going diagrams in the temperature two-particle Green functions are derived at finite temperature. The contribution to the thermodynamic grand potential due to pp-hh RPA correlations is calculated simultaneously to that of ph RPA correlations. A schematic model is constructed which shows that, as for ph RPA states, the energies of pp and hh RPA states have no temperature dependence at not too high temperature. Within the same model, the temperature dependence of the level density parameter is discussed. (orig.)

  3. Annealing helicase HARP closes RPA-stabilized DNA bubbles non-processively

    NARCIS (Netherlands)

    Burnham, D.R.; Nijholt, B.; de Vlaminck, I.; Quan, Jinhua; Yusufzai, Timur; Dekker, C.

    2017-01-01

    We investigate the mechanistic nature of the Snf2 family protein HARP, mutations of which are responsible for Schimke immuno-osseous dysplasia. Using a single-molecule magnetic tweezers assay, we construct RPA-stabilized DNA bubbles within torsionally constrained DNA to investigate the annealing

  4. SOFRA and RPA: two views of the future of southern timber supply.

    Science.gov (United States)

    Darius Adams; John Mills; Ralph Alig; Richard. Haynes

    2005-01-01

    Two recent studies provide alternative views of the current state and future prospects of southern forests and timber supply: the Southern Forest Resource Assessment (SOFRA) and the Fifth Resources Planning Act Timber Assessment (RPA). Using apparently comparable data but different models and methods, the studies portray futures that in some aspects are quite similar...

  5. Tracking the Evolution of "Research & Practice in Assessment" through the Pages of RPA

    Science.gov (United States)

    Anderson, Robin D.; Curtis, Nicolas A.

    2017-01-01

    Ten years ago, "Research & Practice in Assessment" (RPA) was born, providing an outlet for assessment-related research. Since that first winter issue, assessment research and practice has evolved. Like with many evolutions, the assessment practice evolution is best described as a change of emphasis as opposed to a radical revolution.…

  6. Electromagnetic transitions between giant resonances within a continuum-RPA approach

    NARCIS (Netherlands)

    Rodin, VA; Dieperink, AEL

    2002-01-01

    A general continuum-RPA approach is developed to describe electromagnetic transitions between giant resonances. Using a diagrammatic representation for the three-point Green's function, an expression for the transition amplitude is derived which allows one to incorporate effects of mixing of single

  7. U.S. forest products module : a technical document supporting the Forest Service 2010 RPA Assessment

    Science.gov (United States)

    Peter J. Ince; Andrew D. Kramp; Kenneth E. Skog; Henry N. Spelter; David N. Wear

    2011-01-01

    The U.S. Forest Products Module (USFPM) is a partial market equilibrium model of the U.S. forest sector that operates within the Global Forest Products Model (GFPM) to provide long-range timber market projections in relation to global economic scenarios. USFPM was designed specifically for the 2010 RPA forest assessment, but it is being used also in other applications...

  8. RPA and Rad51 constitute a cell intrinsic mechanism to protect the cytosol from self DNA.

    Science.gov (United States)

    Wolf, Christine; Rapp, Alexander; Berndt, Nicole; Staroske, Wolfgang; Schuster, Max; Dobrick-Mattheuer, Manuela; Kretschmer, Stefanie; König, Nadja; Kurth, Thomas; Wieczorek, Dagmar; Kast, Karin; Cardoso, M Cristina; Günther, Claudia; Lee-Kirsch, Min Ae

    2016-05-27

    Immune recognition of cytosolic DNA represents a central antiviral defence mechanism. Within the host, short single-stranded DNA (ssDNA) continuously arises during the repair of DNA damage induced by endogenous and environmental genotoxic stress. Here we show that short ssDNA traverses the nuclear membrane, but is drawn into the nucleus by binding to the DNA replication and repair factors RPA and Rad51. Knockdown of RPA and Rad51 enhances cytosolic leakage of ssDNA resulting in cGAS-dependent type I IFN activation. Mutations in the exonuclease TREX1 cause type I IFN-dependent autoinflammation and autoimmunity. We demonstrate that TREX1 is anchored within the outer nuclear membrane to ensure immediate degradation of ssDNA leaking into the cytosol. In TREX1-deficient fibroblasts, accumulating ssDNA causes exhaustion of RPA and Rad51 resulting in replication stress and activation of p53 and type I IFN. Thus, the ssDNA-binding capacity of RPA and Rad51 constitutes a cell intrinsic mechanism to protect the cytosol from self DNA.

  9. The helicase domain of Polθ counteracts RPA to promote alt-NHEJ.

    Science.gov (United States)

    Mateos-Gomez, Pedro A; Kent, Tatiana; Deng, Sarah K; McDevitt, Shane; Kashkina, Ekaterina; Hoang, Trung M; Pomerantz, Richard T; Sfeir, Agnel

    2017-12-01

    Mammalian polymerase theta (Polθ) is a multifunctional enzyme that promotes error-prone DNA repair by alternative nonhomologous end joining (alt-NHEJ). Here we present structure-function analyses that reveal that, in addition to the polymerase domain, Polθ-helicase activity plays a central role during double-strand break (DSB) repair. Our results show that the helicase domain promotes chromosomal translocations by alt-NHEJ in mouse embryonic stem cells and also suppresses CRISPR-Cas9- mediated gene targeting by homologous recombination (HR). In vitro assays demonstrate that Polθ-helicase activity facilitates the removal of RPA from resected DSBs to allow their annealing and subsequent joining by alt-NHEJ. Consistent with an antagonistic role for RPA during alt-NHEJ, inhibition of RPA1 enhances end joining and suppresses recombination. Taken together, our results reveal that the balance between HR and alt-NHEJ is controlled by opposing activities of Polθ and RPA, providing further insight into the regulation of repair-pathway choice in mammalian cells.

  10. Detection and Characterization of Viral Species/Subspecies Using Isothermal Recombinase Polymerase Amplification (RPA) Assays.

    Science.gov (United States)

    Glais, Laurent; Jacquot, Emmanuel

    2015-01-01

    Numerous molecular-based detection protocols include an amplification step of the targeted nucleic acids. This step is important to reach the expected sensitive detection of pathogens in diagnostic procedures. Amplifications of nucleic acid sequences are generally performed, in the presence of appropriate primers, using thermocyclers. However, the time requested to amplify molecular targets and the cost of the thermocycler machines could impair the use of these methods in routine diagnostics. Recombinase polymerase amplification (RPA) technique allows rapid (short-term incubation of sample and primers in an enzymatic mixture) and simple (isothermal) amplification of molecular targets. RPA protocol requires only basic molecular steps such as extraction procedures and agarose gel electrophoresis. Thus, RPA can be considered as an interesting alternative to standard molecular-based diagnostic tools. In this paper, the complete procedures to set up an RPA assay, applied to detection of RNA (Potato virus Y, Potyvirus) and DNA (Wheat dwarf virus, Mastrevirus) viruses, are described. The proposed procedure allows developing species- or subspecies-specific detection assay.

  11. Isothermal Recombinase Polymerase amplification (RPA) of Schistosoma haematobium DNA and oligochromatographic lateral flow detection.

    Science.gov (United States)

    Rosser, A; Rollinson, D; Forrest, M; Webster, B L

    2015-09-04

    Accurate diagnosis of urogenital schistosomiasis is vital for surveillance/control programs. Amplification of schistosome DNA in urine by PCR is sensitive and specific but requires infrastructure, financial resources and skilled personnel, often not available in endemic areas. Recombinase Polymerase Amplification (RPA) is an isothermal DNA amplification/detection technology that is simple, rapid, portable and needs few resources. Here a Schistosoma haematobium RPA assay was developed and adapted so that DNA amplicons could be detected using oligochromatographic Lateral Flow (LF) strips. The assay successfully amplified S. haematobium DNA at 30-45 °C in 10 mins and was sensitive to a lower limit of 100 fg of DNA. The assay was also successful with the addition of crude urine, up to 5% of the total reaction volume. Cross amplification occurred with other schistosome species but not with other common urine microorganisms. The LF-RPA assay developed here can amplify and detect low levels of S. haematobium DNA. Reactions are rapid, require low temperatures and positive reactions are interpreted using lateral flow strips, reducing the need for infrastructure and resources. This together with an ability to withstand inhibitors within urine makes RPA a promising technology for further development as a molecular diagnostic tool for urogenital schistosomiasis.

  12. Human FAN1 promotes strand incision in 5'-flapped DNA complexed with RPA.

    Science.gov (United States)

    Takahashi, Daisuke; Sato, Koichi; Hirayama, Emiko; Takata, Minoru; Kurumizaka, Hitoshi

    2015-09-01

    Fanconi anaemia (FA) is a human infantile recessive disorder. Seventeen FA causal proteins cooperatively function in the DNA interstrand crosslink (ICL) repair pathway. Dual DNA strand incisions around the crosslink are critical steps in ICL repair. FA-associated nuclease 1 (FAN1) is a DNA structure-specific endonuclease that is considered to be involved in DNA incision at the stalled replication fork. Replication protein A (RPA) rapidly assembles on the single-stranded DNA region of the stalled fork. However, the effect of RPA on the FAN1-mediated DNA incision has not been determined. In this study, we purified human FAN1, as a bacterially expressed recombinant protein. FAN1 exhibited robust endonuclease activity with 5'-flapped DNA, which is formed at the stalled replication fork. We found that FAN1 efficiently promoted DNA incision at the proper site of RPA-coated 5'-flapped DNA. Therefore, FAN1 possesses the ability to promote the ICL repair of 5'-flapped DNA covered by RPA. © The Authors 2015. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

  13. RPA using a multiplexed cartridge for low cost point of care diagnostics in the field.

    Science.gov (United States)

    Ereku, Luck Tosan; Mackay, Ruth E; Craw, Pascal; Naveenathayalan, Angel; Stead, Thomas; Branavan, Manorharanehru; Balachandran, Wamadeva

    2018-04-15

    A point of care device utilising Lab-on-a-Chip technologies that is applicable for biological pathogens was designed, fabricated and tested showing sample in to answer out capabilities. The purpose of the design was to develop a cartridge with the capability to perform nucleic acid extraction and purification from a sample using a chitosan membrane at an acidic pH. Waste was stored within the cartridge with the use of sodium polyacrylate to solidify or gelate the sample in a single chamber. Nucleic acid elution was conducted using the RPA amplification reagents (alkaline pH). Passive valves were used to regulate the fluid flow and a multiplexer was designed to distribute the fluid into six microchambers for amplification reactions. Cartridges were produced using soft lithography of silicone from 3D printed moulds, bonded to glass substrates. The isothermal technique, RPA is employed for amplification. This paper shows the results from two separate experiments: the first using the RPA control nucleic acid, the second showing successful amplification from Chlamydia Trachomatis. Endpoint analysis conducted for the RPA analysis was gel electrophoresis that showed 143 base pair DNA was amplified successfully for positive samples whilst negative samples did not show amplification. End point analysis for Chlamydia Trachomatis samples was fluorescence detection that showed successful detection of 1 copy/μL and 10 copies/μL spiked in a MES buffer. Crown Copyright © 2018. Published by Elsevier Inc. All rights reserved.

  14. BLM helicase measures DNA unwound before switching strands and hRPA promotes unwinding reinitiation

    Czech Academy of Sciences Publication Activity Database

    Yodh, J.G.; Stevens, B.C.; Kanagaraj, R.; Janščák, Pavel; Ha, T.

    2009-01-01

    Roč. 28, č. 4 (2009), s. 405-416 ISSN 0261-4189 Institutional research plan: CEZ:AV0Z50520514 Keywords : Bloom syndrome * FRET * helicase * hRPA * single molecule Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 8.993, year: 2009

  15. Genetic analysis of yeast RPA1 reveals its multiple functions in DNA metabolism

    International Nuclear Information System (INIS)

    Umezu, K.; Sugawara, N.; Chen, C.; Haber, J.E.; Kolodner, R.D.

    1998-01-01

    Replication protein A (RPA) is a single-stranded DNA-binding protein identified as an essential factor for SV40 DNA replication in vitro. To understand the in vivo functions of RPA, we mutagenized the Saccharomyces cerevisiae RFA1 gene and identified 19 ultraviolet light (UV) irradiation- and methyl methane sulfonate (MMS)-sensitive mutants and 5 temperature-sensitive mutants. The UV- and MMS-sensitive mutants showed up to 10 4 to 10 5 times increased sensitivity to these agents. Some of the UV- and MMSsensitive mutants were killed by an HO-induced double-strand break atMAT. Physical analysis of recombination in one UV- and MMS-sensitive rfa1 mutant demonstrated that it was defective for mating type switching and single-strand annealing recombination. Two temperature-sensitive mutants were characterized in detail, and at the restrictive temperature were found to have an arrest phenotype and DNA content indicative of incomplete DNA replication. DNA sequence analysis indicated that most of the mutations altered amino acids that were conserved between yeast, human, and Xenopus RPA1. Taken together, we conclude that RPA1 has multiple roles in vivo and functions in DNA replication, repair, and recombination, like the single-stranded DNA-binding proteins of bacteria and phages. (author)

  16. RPA and XPA interaction with DNA structures mimicking intermediates of the late stages in nucleotide excision repair.

    Science.gov (United States)

    Krasikova, Yuliya S; Rechkunova, Nadejda I; Maltseva, Ekaterina A; Lavrik, Olga I

    2018-01-01

    Replication protein A (RPA) and the xeroderma pigmentosum group A (XPA) protein are indispensable for both pathways of nucleotide excision repair (NER). Here we analyze the interaction of RPA and XPA with DNA containing a flap and different size gaps that imitate intermediates of the late NER stages. Using gel mobility shift assays, we found that RPA affinity for DNA decreased when DNA contained both extended gap and similar sized flap in comparison with gapped-DNA structure. Moreover, crosslinking experiments with the flap-gap DNA revealed that RPA interacts mainly with the ssDNA platform within the long gap and contacts flap in DNA with a short gap. XPA exhibits higher affinity for bubble-DNA structures than to flap-gap-containing DNA. Protein titration analysis showed that formation of the RPA-XPA-DNA ternary complex depends on the protein concentration ratio and these proteins can function as independent players or in tandem. Using fluorescently-labelled RPA, direct interaction of this protein with XPA was detected and characterized quantitatively. The data obtained allow us to suggest that XPA can be involved in the post-incision NER stages via its interaction with RPA.

  17. Replication-mediated disassociation of replication protein A–XPA complex upon DNA damage: implications for RPA handing off

    Science.gov (United States)

    Jiang, Gaofeng; Zou, Yue; Wu, Xiaoming

    2013-01-01

    RPA (replication protein A), the eukaryotic ssDNA (single-stranded DNA)-binding protein, participates in most cellular processes in response to genotoxic insults, such as NER (nucleotide excision repair), DNA, DSB (double-strand break) repair and activation of cell cycle checkpoint signalling. RPA interacts with XPA (xeroderma pigmentosum A) and functions in early stage of NER. We have shown that in cells the RPA–XPA complex disassociated upon exposure of cells to high dose of UV irradiation. The dissociation required replication stress and was partially attributed to tRPA hyperphosphorylation. Treatment of cells with CPT (camptothecin) and HU (hydroxyurea), which cause DSB DNA damage and replication fork collapse respectively and also leads to the disruption of RPA–XPA complex. Purified RPA and XPA were unable to form complex in vitro in the presence of ssDNA. We propose that the competition-based RPA switch among different DNA metabolic pathways regulates the dissociation of RPA with XPA in cells after DNA damage. The biological significances of RPA–XPA complex disruption in relation with checkpoint activation, DSB repair and RPA hyperphosphorylation are discussed. PMID:22578086

  18. RPA and XPA interaction with DNA structures mimicking intermediates of the late stages in nucleotide excision repair.

    Directory of Open Access Journals (Sweden)

    Yuliya S Krasikova

    Full Text Available Replication protein A (RPA and the xeroderma pigmentosum group A (XPA protein are indispensable for both pathways of nucleotide excision repair (NER. Here we analyze the interaction of RPA and XPA with DNA containing a flap and different size gaps that imitate intermediates of the late NER stages. Using gel mobility shift assays, we found that RPA affinity for DNA decreased when DNA contained both extended gap and similar sized flap in comparison with gapped-DNA structure. Moreover, crosslinking experiments with the flap-gap DNA revealed that RPA interacts mainly with the ssDNA platform within the long gap and contacts flap in DNA with a short gap. XPA exhibits higher affinity for bubble-DNA structures than to flap-gap-containing DNA. Protein titration analysis showed that formation of the RPA-XPA-DNA ternary complex depends on the protein concentration ratio and these proteins can function as independent players or in tandem. Using fluorescently-labelled RPA, direct interaction of this protein with XPA was detected and characterized quantitatively. The data obtained allow us to suggest that XPA can be involved in the post-incision NER stages via its interaction with RPA.

  19. Effects of depletion of dihydropyrimidine dehydrogenase on focus formation and RPA phosphorylation.

    Science.gov (United States)

    Someya, Masanori; Sakata, Koh-ichi; Matsumoto, Yoshihisa; Tauchi, Hiroshi; Kai, Masahiro; Hareyama, Masato; Fukushima, Masakazu

    2012-01-01

    Gimeracil, an inhibitor of dihydropyrimidine dehydrogenase (DPYD), partially inhibits homologous recombination (HR) repair and has a radiosensitizing effect as well as enhanced sensitivity to Camptothecin (CPT). DPYD is the target protein for radiosensitization by Gimeracil. We investigated the mechanisms of sensitization of radiation and CPT by DPYD inhibition using DLD-1 cells treated with siRNA for DPYD. We investigated the focus formation of various kinds of proteins involved in HR and examined the phosphorylation of RPA by irradiation using Western blot analysis. DPYD depletion by siRNA significantly restrained the formation of radiation-induced foci of Rad51 and RPA, whereas it increased the number of foci of NBS1. The numbers of colocalization of NBS1 and RPA foci in DPYD-depleted cells after radiation were significantly smaller than in the control cells. These results suggest that DPYD depletion is attributable to decreased single-stranded DNA generated by the Mre11/Rad50/NBS1 complex-dependent resection of DNA double-strand break ends. The phosphorylation of RPA by irradiation was partially suppressed in DPYD-depleted cells, suggesting that DPYD depletion may partially inhibit DNA repair with HR by suppressing phosphorylation of RPA. DPYD depletion showed a radiosensitizing effect as well as enhanced sensitivity to CPT. The radiosensitizing effect of DPYD depletion plus CPT was the additive effect of DPYD depletion and CPT. DPYD depletion did not have a cell-killing effect, suggesting that DPYD depletion may not be so toxic. Considering these results, the combination of CPT and drugs that inhibit DPYD may prove useful for radiotherapy as a method of radiosensitization.

  20. Factors influencing Recombinase polymerase amplification (RPA) assay outcomes at point of care.

    Science.gov (United States)

    Lillis, Lorraine; Siverson, Joshua; Lee, Arthur; Cantera, Jason; Parker, Mathew; Piepenburg, Olaf; Lehman, Dara A; Boyle, David S

    2016-04-01

    Recombinase Polymerase Amplification (RPA) can be used to detect pathogen-specific DNA or RNA in under 20 min without the need for complex instrumentation. These properties enable its potential use in resource limited settings. However, there are concerns that deviations from the manufacturer's protocol and/or storage conditions could influence its performance in low resource settings. RPA amplification relies upon viscous crowding agents for optimal nucleic acid amplification, and thus an interval mixing step after 3-6 min of incubation is recommended to distribute amplicons and improve performance. In this study we used a HIV-1 RPA assay to evaluate the effects of this mixing step on assay performance. A lack of mixing led to a longer time to amplification and inferior detection signal, compromising the sensitivity of the assay. However lowering the assay volume from 50 μL to 5 μL showed similar sensitivity with or without mixing. We present the first peer-reviewed study that assesses long term stability of RPA reagents without a cold chain. Reagents stored at -20 °C, and 25 °C for up to 12 weeks were able to detect 10 HIV-1 DNA copies. Reagents stored at 45 °C for up to 3 weeks were able to detect 10 HIV-1 DNA copies, with reduced sensitivity only after >3 weeks at 45 °C. Together our results show that reducing reaction volumes bypassed the need for the mixing step and that RPA reagents were stable even when stored for 3 weeks at very high temperatures. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Recursive partitioning analysis (RPA) classification predicts survival in patients with brain metastases from sarcoma.

    Science.gov (United States)

    Grossman, Rachel; Ram, Zvi

    2014-12-01

    Sarcoma rarely metastasizes to the brain, and there are no specific treatment guidelines for these tumors. The recursive partitioning analysis (RPA) classification is a well-established prognostic scale used in many malignancies. In this study we assessed the clinical characteristics of metastatic sarcoma to the brain and the validity of the RPA classification system in a subset of 21 patients who underwent surgical resection of metastatic sarcoma to the brain We retrospectively analyzed the medical, radiological, surgical, pathological, and follow-up clinical records of 21 patients who were operated for metastatic sarcoma to the brain between 1996 and 2012. Gliosarcomas, sarcomas of the head and neck with local extension into the brain, and metastatic sarcomas to the spine were excluded from this reported series. The patients' mean age was 49.6 ± 14.2 years (range, 25-75 years) at the time of diagnosis. Sixteen patients had a known history of systemic sarcoma, mostly in the extremities, and had previously received systemic chemotherapy and radiation therapy for their primary tumor. The mean maximal tumor diameter in the brain was 4.9 ± 1.7 cm (range 1.7-7.2 cm). The group's median preoperative Karnofsky Performance Scale was 80, with 14 patients presenting with Karnofsky Performance Scale of 70 or greater. The median overall survival was 7 months (range 0.2-204 months). The median survival time stratified by the Radiation Therapy Oncology Group RPA classes were 31, 7, and 2 months for RPA class I, II, and III, respectively (P = 0.0001). This analysis is the first to support the prognostic utility of the Radiation Therapy Oncology Group RPA classification for sarcoma brain metastases and may be used as a treatment guideline tool in this rare disease. Copyright © 2014 Elsevier Inc. All rights reserved.

  2. TERRA and hnRNPA1 orchestrate an RPA-to-POT1 switch on telomeric single-stranded DNA.

    Science.gov (United States)

    Flynn, Rachel Litman; Centore, Richard C; O'Sullivan, Roderick J; Rai, Rekha; Tse, Alice; Songyang, Zhou; Chang, Sandy; Karlseder, Jan; Zou, Lee

    2011-03-24

    Maintenance of telomeres requires both DNA replication and telomere 'capping' by shelterin. These two processes use two single-stranded DNA (ssDNA)-binding proteins, replication protein A (RPA) and protection of telomeres 1 (POT1). Although RPA and POT1 each have a critical role at telomeres, how they function in concert is not clear. POT1 ablation leads to activation of the ataxia telangiectasia and Rad3-related (ATR) checkpoint kinase at telomeres, suggesting that POT1 antagonizes RPA binding to telomeric ssDNA. Unexpectedly, we found that purified POT1 and its functional partner TPP1 are unable to prevent RPA binding to telomeric ssDNA efficiently. In cell extracts, we identified a novel activity that specifically displaces RPA, but not POT1, from telomeric ssDNA. Using purified protein, here we show that the heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) recapitulates the RPA displacing activity. The RPA displacing activity is inhibited by the telomeric repeat-containing RNA (TERRA) in early S phase, but is then unleashed in late S phase when TERRA levels decline at telomeres. Interestingly, TERRA also promotes POT1 binding to telomeric ssDNA by removing hnRNPA1, suggesting that the re-accumulation of TERRA after S phase helps to complete the RPA-to-POT1 switch on telomeric ssDNA. Together, our data suggest that hnRNPA1, TERRA and POT1 act in concert to displace RPA from telomeric ssDNA after DNA replication, and promote telomere capping to preserve genomic integrity.

  3. Two correlated quasiparticles states in the principal series approximation

    International Nuclear Information System (INIS)

    Dukelsky, J.; Dussel, G.G.; Sofia, H.M.

    1983-01-01

    The principal series approximation is extended to the description of two correlated quasiparticles states, enabling a treatment of these states that takes into account the coupling among the two particle Green's function and the particle-hole one. This description is related to a random phase approximation treatment of collective states in open shell nuclei that includes simultaneously the particle-particle and particle-hole versions of the nuclear residual Hamiltonian. Using separable interactions it is found that the inclusion of the particle-particle part of the Hamiltonians greatly changes the properties of the 2 + states in the Sn isotopes

  4. RPA70 depletion induces hSSB1/2-INTS3 complex to initiate ATR signaling

    OpenAIRE

    Kar, Ananya; Kaur, Manpreet; Ghosh, Tanushree; Khan, Md. Muntaz; Sharma, Aparna; Shekhar, Ritu; Varshney, Akhil; Saxena, Sandeep

    2015-01-01

    The primary eukaryotic single-stranded DNA-binding protein, Replication protein A (RPA), binds to single-stranded DNA at the sites of DNA damage and recruits the apical checkpoint kinase, ATR via its partner protein, ATRIP. It has been demonstrated that absence of RPA incapacitates the ATR-mediated checkpoint response. We report that in the absence of RPA, human single-stranded DNA-binding protein 1 (hSSB1) and its partner protein INTS3 form sub-nuclear foci, associate with the ATR-ATRIP comp...

  5. Nonlinear generalization of the quasiparticle random phase approximation for description of anharmonic effects in vibrational spectra: Application to the even Ni isotopes

    International Nuclear Information System (INIS)

    Li, C.T.; Klein, A.

    1979-01-01

    The theory of anharmonic nuclear vibrational motion (nonlinear equations-of-motion method) developed in the preceding paper is applied to atsup 60,62,64atNi, which exhibit one and two phonon quadrupole collective states. A model Hamiltonian consisting of a modified pairing plus quadrupole interaction is studied first by comparing the results of the nonlinear equations-of-motion method with those of an exact diagonalization. Contrary to popular opinion, the model chosen fails to produce a vibrational spectrum, except in the case of 60 Ni, and as a consequence, the nonlinear equations-of-motion method, designed specifically to describe vibrational spectra, accords well with the exact calculations only for this case. A simple method is then described, within the framework of the nonlinear equations-of-motion method, for refining the model Hamiltonian so as to bring it into accord with experiment. In practice, it is found that a simple additional parameter in the Hamiltonian suffices to yield descriptions of the quadrupole states in Ni isotopes comparable in precision to the most up-to-date versions (modified, adjusted, etc.) of the surface delta interaction model

  6. IDN2 Interacts with RPA and Facilitates DNA Double-Strand Break Repair by Homologous Recombination in Arabidopsis.

    Science.gov (United States)

    Liu, Mingming; Ba, Zhaoqing; Costa-Nunes, Pedro; Wei, Wei; Li, Lanxia; Kong, Fansi; Li, Yan; Chai, Jijie; Pontes, Olga; Qi, Yijun

    2017-03-01

    Repair of DNA double-strand breaks (DSBs) is critical for the maintenance of genome integrity. We previously showed that DSB-induced small RNAs (diRNAs) facilitate homologous recombination-mediated DSB repair in Arabidopsis thaliana Here, we show that INVOLVED IN DE NOVO2 (IDN2), a double-stranded RNA binding protein involved in small RNA-directed DNA methylation, is required for DSB repair in Arabidopsis. We find that IDN2 interacts with the heterotrimeric replication protein A (RPA) complex. Depletion of IDN2 or the diRNA binding ARGONAUTE2 leads to increased accumulation of RPA at DSB sites and mislocalization of the recombination factor RAD51. These findings support a model in which IDN2 interacts with RPA and facilitates the release of RPA from single-stranded DNA tails and subsequent recruitment of RAD51 at DSB sites to promote DSB repair. © 2017 American Society of Plant Biologists. All rights reserved.

  7. Local Treatment of Unresectable Colorectal Liver Metastases: Results of a Randomized Phase II Trial.

    Science.gov (United States)

    Ruers, Theo; Van Coevorden, Frits; Punt, Cornelis J A; Pierie, Jean-Pierre E N; Borel-Rinkes, Inne; Ledermann, Jonathan A; Poston, Graeme; Bechstein, Wolf; Lentz, Marie-Ange; Mauer, Murielle; Folprecht, Gunnar; Van Cutsem, Eric; Ducreux, Michel; Nordlinger, Bernard

    2017-09-01

    Tumor ablation is often employed for unresectable colorectal liver metastases. However, no survival benefit has ever been demonstrated in prospective randomized studies. Here, we investigate the long-term benefits of such an aggressive approach. In this randomized phase II trial, 119 patients with unresectable colorectal liver metastases (n  38%) was met. We now report on long-term OS results. All statistical tests were two-sided. The analyses were according to intention to treat. At a median follow up of 9.7 years, 92 of 119 (77.3%) patients had died: 39 of 60 (65.0%) in the combined modality arm and 53 of 59 (89.8%) in the systemic treatment arm. Almost all patients died of progressive disease (35 patients in the combined modality arm, 49 patients in the systemic treatment arm). There was a statistically significant difference in OS in favor of the combined modality arm (hazard ratio [HR] = 0.58, 95% confidence interval [CI] = 0.38 to 0.88, P = .01). Three-, five-, and eight-year OS were 56.9% (95% CI = 43.3% to 68.5%), 43.1% (95% CI = 30.3% to 55.3%), 35.9% (95% CI = 23.8% to 48.2%), respectively, in the combined modality arm and 55.2% (95% CI = 41.6% to 66.9%), 30.3% (95% CI = 19.0% to 42.4%), 8.9% (95% CI = 3.3% to 18.1%), respectively, in the systemic treatment arm. Median OS was 45.6 months (95% CI = 30.3 to 67.8 months) in the combined modality arm vs 40.5 months (95% CI = 27.5 to 47.7 months) in the systemic treatment arm. This phase II trial is the first randomized study demonstrating that aggressive local treatment can prolong OS in patients with unresectable colorectal liver metastases. © The Author 2017. Published by Oxford University Press.

  8. Pharmacokinetics and Safety of Amenamevir in Healthy Subjects: Analysis of Four Randomized Phase 1 Studies.

    Science.gov (United States)

    Kusawake, Tomohiro; Keirns, James J; Kowalski, Donna; den Adel, Martin; Groenendaal-van de Meent, Dorien; Takada, Akitsugu; Ohtsu, Yoshiaki; Katashima, Masataka

    2017-12-01

    Amenamevir (ASP2151) is a nonnucleoside antiherpesvirus compound available for the treatment of varicella-zoster virus infections. In this article we summarize the findings of four phase 1 studies in healthy participants. Four randomized phase 1 studies investigated the safety and pharmacokinetics of single and multiple doses of amenamevir, including the assessment of age group effect (nonelderly vs elderly), food effect, and the relative bioavailability of two formulations. Amenamevir was administered orally at various doses as a single dose (5-2400 mg) or daily (300 or 600 mg/day) for 7 days. Following single and multiple oral doses, amenamevir demonstrated a less than dose proportional increase in the pharmacokinetic parameters area under the plasma drug concentration versus time curve from time zero to infinity (AUC inf ) and C max . After single and multiple oral 300-mg doses of amenamevir, no apparent differences in pharmacokinetics were observed between nonelderly and elderly participants. In contrast, with the amenamevir 600-mg dose both the area under the plasma drug concentration versus time curve from time zero to 24 h and C max were slightly increased and renal clearance was decreased in elderly participants. The pharmacokinetics of amenamevir was affected by food, with AUC inf increased by about 90%. In the bioavailability study, AUC inf and C max were slightly lower following tablet versus capsule administration (decreased by 14 and 12%, respectively), with relative bioavailability of 86%. The different amenamevir doses and formulations were safe and well tolerated; no deaths or serious adverse events were reported. Amenamevir had less than dose proportional pharmacokinetic characteristics. Age may have an influence on amenamevir pharmacokinetics; however, the effect was considered minimal. The pharmacokinetics of amenamevir were affected by food, with AUC inf almost doubling when amenamevir was administered with food. The concentration versus

  9. Recombinase polymerase amplification (RPA) combined with lateral flow (LF) strip for detection of Toxoplasma gondii in the environment.

    Science.gov (United States)

    Wu, Y D; Xu, M J; Wang, Q Q; Zhou, C X; Wang, M; Zhu, X Q; Zhou, D H

    2017-08-30

    Toxoplasma gondii infects all warm-blooded vertebrates, resulting in a great threat to human health and significant economic loss to the livestock industry. Ingestion of infectious oocysts of T. gondii from the environment is the major source of transmission. Detection of T. gondii oocysts by existing methods is laborious, time-consuming and expensive. The objective of the present study was to develop a recombinase polymerase amplification (RPA) method combined with a lateral flow (LF) strip for detection of T. gondii oocysts in the soil and water. The DNA of T. gondii oocysts was amplified by a pair of specific primers based on the T. gondii B1 gene over 15min at a constant temperature ranging from 30°C to 45°C using RPA. The amplification product was visualized by the lateral flow (LF) strip within 5min using the specific probe added to the RPA reaction system. The sensitivity of the established assay was 10 times higher than that of nested PCR with a lower detection limit of 0.1 oocyst per reaction, and there was no cross-reactivity with other closely related protozoan species. Fifty environmental samples were further assessed for the detection validity of the LF-RPA assay (B1-LF-RPA) and compared with nested PCR based on the B1 gene sequence. The B1-LF-RPA and nested PCR both showed that 5 out of the 50 environmental samples were positive. The B1-LF-RPA method was also proven to be sufficiently tolerant of existing inhibitors in the environment. In addition, the advantages of simple operation, speediness and cost-effectiveness make B1-LF-RPA a promising molecular detection tool for T. gondii. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Replication protein A (RPA) hampers the processive action of APOBEC3G cytosine deaminase on single-stranded DNA.

    Science.gov (United States)

    Lada, Artem G; Waisertreiger, Irina S-R; Grabow, Corinn E; Prakash, Aishwarya; Borgstahl, Gloria E O; Rogozin, Igor B; Pavlov, Youri I

    2011-01-01

    Editing deaminases have a pivotal role in cellular physiology. A notable member of this superfamily, APOBEC3G (A3G), restricts retroviruses, and Activation Induced Deaminase (AID) generates antibody diversity by localized deamination of cytosines in DNA. Unconstrained deaminase activity can cause genome-wide mutagenesis and cancer. The mechanisms that protect the genomic DNA from the undesired action of deaminases are unknown. Using the in vitro deamination assays and expression of A3G in yeast, we show that replication protein A (RPA), the eukaryotic single-stranded DNA (ssDNA) binding protein, severely inhibits the deamination activity and processivity of A3G. We found that mutations induced by A3G in the yeast genomic reporter are changes of a single nucleotide. This is unexpected because of the known property of A3G to catalyze multiple deaminations upon one substrate encounter event in vitro. The addition of recombinant RPA to the oligonucleotide deamination assay severely inhibited A3G activity. Additionally, we reveal the inverse correlation between RPA concentration and the number of deaminations induced by A3G in vitro on long ssDNA regions. This resembles the "hit and run" single base substitution events observed in yeast. Our data suggest that RPA is a plausible antimutator factor limiting the activity and processivity of editing deaminases in the model yeast system. Because of the similar antagonism of yeast RPA and human RPA with A3G in vitro, we propose that RPA plays a role in the protection of the human genome cell from A3G and other deaminases when they are inadvertently diverged from their natural targets. We propose a model where RPA serves as one of the guardians of the genome that protects ssDNA from the destructive processive activity of deaminases by non-specific steric hindrance.

  11. Replication protein A (RPA hampers the processive action of APOBEC3G cytosine deaminase on single-stranded DNA.

    Directory of Open Access Journals (Sweden)

    Artem G Lada

    Full Text Available Editing deaminases have a pivotal role in cellular physiology. A notable member of this superfamily, APOBEC3G (A3G, restricts retroviruses, and Activation Induced Deaminase (AID generates antibody diversity by localized deamination of cytosines in DNA. Unconstrained deaminase activity can cause genome-wide mutagenesis and cancer. The mechanisms that protect the genomic DNA from the undesired action of deaminases are unknown. Using the in vitro deamination assays and expression of A3G in yeast, we show that replication protein A (RPA, the eukaryotic single-stranded DNA (ssDNA binding protein, severely inhibits the deamination activity and processivity of A3G.We found that mutations induced by A3G in the yeast genomic reporter are changes of a single nucleotide. This is unexpected because of the known property of A3G to catalyze multiple deaminations upon one substrate encounter event in vitro. The addition of recombinant RPA to the oligonucleotide deamination assay severely inhibited A3G activity. Additionally, we reveal the inverse correlation between RPA concentration and the number of deaminations induced by A3G in vitro on long ssDNA regions. This resembles the "hit and run" single base substitution events observed in yeast.Our data suggest that RPA is a plausible antimutator factor limiting the activity and processivity of editing deaminases in the model yeast system. Because of the similar antagonism of yeast RPA and human RPA with A3G in vitro, we propose that RPA plays a role in the protection of the human genome cell from A3G and other deaminases when they are inadvertently diverged from their natural targets. We propose a model where RPA serves as one of the guardians of the genome that protects ssDNA from the destructive processive activity of deaminases by non-specific steric hindrance.

  12. Ionizing radiation-induced phosphorylation of RPA p34 is deficient in ataxia telangiectasia and reduced in aged normal fibroblasts

    International Nuclear Information System (INIS)

    Xinbo Cheng; Nge Cheong; Ya Wang; Iliakis, George

    1996-01-01

    Replication protein A (RPA, also called human single stranded DNA binding protein, hSSB) is a trimeric, multifunctional protein complex involved in DNA replication, DNA repair and recombination. Phosphorylation of RPA p34 subunit is observed after exposure of cells to radiation and other DNA damaging agents, which implicates the protein not only in repair but also in the regulation of replication on damaged DNA template. Here, we show that the phosphorylation observed in RPA p34 after exposure to ionizing radiation, X- or γ-rays, is reduced and occurs later in primary fibroblasts from patients suffering from ataxia telangiectasia (AT), as compared to normal fibroblasts. We also show that in primary normal human fibroblasts, radiation-induced phosphorylation of RPA p34 is 'age'-dependent and decreases significantly as cultures senesce. Radiation-induced phosphorylation of RPA p34 is nearly absent in non-cycling cells, while the expression of p21 cip1/waf1/sdi1 remains inducible. The results demonstrate a growth-stage and culture-age dependency in radiation-induced RPA p34 phosphorylation, and suggest the operation of a signal transduction pathway that is inactivated in senescing or quiescent fibroblasts and defective in AT cells

  13. A Shld1-controlled POT1a provides support for repression of ATR signaling at telomeres through RPA exclusion.

    Science.gov (United States)

    Gong, Yi; de Lange, Titia

    2010-11-12

    We previously proposed that POT1 prevents ATR signaling at telomeres by excluding RPA from the single-stranded TTAGGG repeats. Here, we use a Shld1-stabilized degron-POT1a fusion (DD-POT1a) to study the telomeric ATR kinase response. In the absence of Shld1, DD-POT1a degradation resulted in rapid and reversible activation of the ATR pathway in G1 and S/G2. ATR signaling was abrogated by shRNAs to ATR and TopBP1, but shRNAs to the ATM kinase or DNA-PKcs did not affect the telomere damage response. Importantly, ATR signaling in G1 and S/G2 was reduced by shRNAs to RPA. In S/G2, RPA was readily detectable at dysfunctional telomeres, and both POT1a and POT1b were required to exclude RPA and prevent ATR activation. In G1, the accumulation of RPA at dysfunctional telomeres was strikingly less, and POT1a was sufficient to repress ATR signaling. These results support an RPA exclusion model for the repression of ATR signaling at telomeres. Copyright © 2010 Elsevier Inc. All rights reserved.

  14. RPA Interacts with HIRA and Regulates H3.3 Deposition at Gene Regulatory Elements in Mammalian Cells.

    Science.gov (United States)

    Zhang, Honglian; Gan, Haiyun; Wang, Zhiquan; Lee, Jeong-Heon; Zhou, Hui; Ordog, Tamas; Wold, Marc S; Ljungman, Mats; Zhang, Zhiguo

    2017-01-19

    The histone chaperone HIRA is involved in depositing histone variant H3.3 into distinct genic regions, including promoters, enhancers, and gene bodies. However, how HIRA deposits H3.3 to these regions remains elusive. Through a short hairpin RNA (shRNA) screening, we identified single-stranded DNA binding protein replication protein A (RPA) as a regulator of the deposition of newly synthesized H3.3 into chromatin. We show that RPA physically interacts with HIRA to form RPA-HIRA-H3.3 complexes, and it co-localizes with HIRA and H3.3 at gene promoters and enhancers. Depletion of RPA1, the largest subunit of the RPA complex, dramatically reduces both HIRA association with chromatin and the deposition of newly synthesized H3.3 at promoters and enhancers and leads to altered transcription at gene promoters. These results support a model whereby RPA, best known for its role in DNA replication and repair, recruits HIRA to promoters and enhancers and regulates deposition of newly synthesized H3.3 to these regulatory elements for gene regulation. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. RPA-Mediated Recruitment of the E3 Ligase RFWD3 Is Vital for Interstrand Crosslink Repair and Human Health.

    Science.gov (United States)

    Feeney, Laura; Muñoz, Ivan M; Lachaud, Christophe; Toth, Rachel; Appleton, Paul L; Schindler, Detlev; Rouse, John

    2017-06-01

    Defects in the repair of DNA interstrand crosslinks (ICLs) are associated with the genome instability syndrome Fanconi anemia (FA). Here we report that cells with mutations in RFWD3, an E3 ubiquitin ligase that interacts with and ubiquitylates replication protein A (RPA), show profound defects in ICL repair. An amino acid substitution in the WD40 repeats of RFWD3 (I639K) found in a new FA subtype abolishes interaction of RFWD3 with RPA, thereby preventing RFWD3 recruitment to sites of ICL-induced replication fork stalling. Moreover, single point mutations in the RPA32 subunit of RPA that abolish interaction with RFWD3 also inhibit ICL repair, demonstrating that RPA-mediated RFWD3 recruitment to stalled replication forks is important for ICL repair. We also report that unloading of RPA from sites of ICL induction is perturbed in RFWD3-deficient cells. These data reveal important roles for RFWD3 localization in protecting genome stability and preserving human health. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  16. Recombinant protective antigen 102 (rPA102): profile of a second-generation anthrax vaccine.

    Science.gov (United States)

    Keitel, Wendy A

    2006-08-01

    Recent terrorist attacks involving the use of Bacillus anthracis spores have stimulated interest in the development of new vaccines for anthrax prevention. Studies of the pathogenesis of anthrax and of the immune responses following infection and immunization underscore the pivotal role that antibodies to the protective antigen play in protection. The most promising vaccine candidates contain purified recombinant protective antigen. Clinical trials of one of these, recombinant protective antigen (rPA)102, are underway. Initial results suggest that rPA102 is well tolerated and immunogenic. Additional trials are necessary to identify optimal formulations and immunization regimens for pre- and postexposure prophylaxis. Future licensure of these and other candidate vaccines will depend on their safety and immunogenicity profiles in humans, and their ability to confer protection in animal models of inhalational anthrax.

  17. Self-consistent quasi-particle RPA for the description of superfluid Fermi systems

    CERN Document Server

    Rahbi, A; Chanfray, G; Schuck, P

    2002-01-01

    Self-Consistent Quasi-Particle RPA (SCQRPA) is for the first time applied to a more level pairing case. Various filling situation and values for the coupling constant are considered. Very encouraging results in comparison with the exact solution of the model are obtaining. The nature of the low lying mode in SCQRPA is identified. The strong reduction of the number fluctuation in SCQRPA vs BCS is pointed out. The transition from superfluidity to the normal fluid case is carefully investigated.

  18. Hybrid RPA-cluster model for the dipole strength function of sup(11)Li

    International Nuclear Information System (INIS)

    Teruya, N.; Bertulani, C.A.; Krewald, S.

    1990-09-01

    A hybrid RPA-cluster model is developed and applied to the calculation of the dipole response of sup(11)L1. A strong collective state at 1.81 MeV is found. Its width is predicted to be 4.0 MeV. The electromagnetic excitation cross section was found to be 700 mb for sup(11)L1 + sup(208)Pb (E = 800 MeV/n), close to the experimental result. (author)

  19. RPA spin-isospin nuclear response in the deep inelastic region

    International Nuclear Information System (INIS)

    Alberico, W.M.; Molinari, A.; De Pace, A.; Johnson, M.B.; Ericson, M.

    1985-11-01

    The spin-isospin volume responses of a finite nucleus are evaluated in the RPA frame, utilizing a harmonic oscillator basis. Particular emphasis is given to the mixing between the longitudinal and transverse couplings, which arise at the nuclear surface. We show that it reduces somewhat the contrast between the two spin responses. We compare the calculated transverse response with the experimental one extracted from deep inelastic electron scattering

  20. Molecular basis for PrimPol recruitment to replication forks by RPA.

    Science.gov (United States)

    Guilliam, Thomas A; Brissett, Nigel C; Ehlinger, Aaron; Keen, Benjamin A; Kolesar, Peter; Taylor, Elaine M; Bailey, Laura J; Lindsay, Howard D; Chazin, Walter J; Doherty, Aidan J

    2017-05-23

    DNA damage and secondary structures can stall the replication machinery. Cells possess numerous tolerance mechanisms to complete genome duplication in the presence of such impediments. In addition to translesion synthesis (TLS) polymerases, most eukaryotic cells contain a multifunctional replicative enzyme called primase-polymerase (PrimPol) that is capable of directly bypassing DNA damage by TLS, as well as repriming replication downstream of impediments. Here, we report that PrimPol is recruited to reprime through its interaction with RPA. Using biophysical and crystallographic approaches, we identify that PrimPol possesses two RPA-binding motifs and ascertained the key residues required for these interactions. We demonstrate that one of these motifs is critical for PrimPol's recruitment to stalled replication forks in vivo. In addition, biochemical analysis reveals that RPA serves to stimulate the primase activity of PrimPol. Together, these findings provide significant molecular insights into PrimPol's mode of recruitment to stalled forks to facilitate repriming and restart.

  1. G-quadruplex formation in telomeres enhances POT1/TPP1 protection against RPA binding

    Science.gov (United States)

    Ray, Sujay; Bandaria, Jigar N.; Qureshi, Mohammad H.; Yildiz, Ahmet; Balci, Hamza

    2014-01-01

    Human telomeres terminate with a single-stranded 3′ G overhang, which can be recognized as a DNA damage site by replication protein A (RPA). The protection of telomeres (POT1)/POT1-interacting protein 1 (TPP1) heterodimer binds specifically to single-stranded telomeric DNA (ssTEL) and protects G overhangs against RPA binding. The G overhang spontaneously folds into various G-quadruplex (GQ) conformations. It remains unclear whether GQ formation affects the ability of POT1/TPP1 to compete against RPA to access ssTEL. Using single-molecule Förster resonance energy transfer, we showed that POT1 stably loads to a minimal DNA sequence adjacent to a folded GQ. At 150 mM K+, POT1 loading unfolds the antiparallel GQ, as the parallel conformation remains folded. POT1/TPP1 loading blocks RPA’s access to both folded and unfolded telomeres by two orders of magnitude. This protection is not observed at 150 mM Na+, in which ssTEL forms only a less-stable antiparallel GQ. These results suggest that GQ formation of telomeric overhangs may contribute to suppression of DNA damage signals. PMID:24516170

  2. RPA Stabilization of Single-Stranded DNA Is Critical for Break-Induced Replication.

    Science.gov (United States)

    Ruff, Patrick; Donnianni, Roberto A; Glancy, Eleanor; Oh, Julyun; Symington, Lorraine S

    2016-12-20

    DNA double-strand breaks (DSBs) are cytotoxic lesions that must be accurately repaired to maintain genome stability. Replication protein A (RPA) plays an important role in homology-dependent repair of DSBs by protecting the single-stranded DNA (ssDNA) intermediates formed by end resection and by facilitating Rad51 loading. We found that hypomorphic mutants of RFA1 that support intra-chromosomal homologous recombination are profoundly defective for repair processes involving long tracts of DNA synthesis, in particular break-induced replication (BIR). The BIR defects of the rfa1 mutants could be partially suppressed by eliminating the Sgs1-Dna2 resection pathway, suggesting that Dna2 nuclease attacks the ssDNA formed during end resection when not fully protected by RPA. Overexpression of Rad51 was also found to suppress the rfa1 BIR defects. We suggest that Rad51 binding to the ssDNA formed by excessive end resection and during D-loop migration can partially compensate for dysfunctional RPA. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  3. RPA activates the XPF-ERCC1 endonuclease to initiate processing of DNA interstrand crosslinks.

    Science.gov (United States)

    Abdullah, Ummi B; McGouran, Joanna F; Brolih, Sanja; Ptchelkine, Denis; El-Sagheer, Afaf H; Brown, Tom; McHugh, Peter J

    2017-07-14

    During replication-coupled DNA interstrand crosslink (ICL) repair, the XPF-ERCC1 endonuclease is required for the incisions that release, or "unhook", ICLs, but the mechanism of ICL unhooking remains largely unknown. Incisions are triggered when the nascent leading strand of a replication fork strikes the ICL Here, we report that while purified XPF-ERCC1 incises simple ICL-containing model replication fork structures, the presence of a nascent leading strand, modelling the effects of replication arrest, inhibits this activity. Strikingly, the addition of the single-stranded DNA (ssDNA)-binding replication protein A (RPA) selectively restores XPF-ERCC1 endonuclease activity on this structure. The 5'-3' exonuclease SNM1A can load from the XPF-ERCC1-RPA-induced incisions and digest past the crosslink to quantitatively complete the unhooking reaction. We postulate that these collaborative activities of XPF-ERCC1, RPA and SNM1A might explain how ICL unhooking is achieved in vivo . © 2017 The Authors. Published under the terms of the CC BY 4.0 license.

  4. Nonergodic dynamics of the two-dimensional random-phase sine-Gordon model: Applications to vortex-glass arrays and disordered-substrate surfaces

    International Nuclear Information System (INIS)

    Cule, D.; Shapir, Y.

    1995-01-01

    The dynamics of the random-phase sine-Gordon model, which describes two-dimensional vortex-glass arrays and crystalline surfaces on disordered substrates, is investigated using the self-consistent Hartree approximation. The fluctuation-dissipation theorem is violated below the critical temperature T c for large time t>t * where t * diverges in the thermodynamic limit. While above T c the averaged autocorrelation function diverges as Tln(t), for T c it approaches a finite value q * ∼1/(T c -T) as q(t)=q * -c(t/t * ) -ν (for t→t * ) where ν is a temperature-dependent exponent. On larger time scales t>t * the dynamics becomes nonergodic. The static correlations behave as ∼Tln|rvec x| for T>T c and for T c when x * with ξ * ∼exp{A/(T c -T)}. For scales x>ξ * , they behave as ∼m -1 Tln|rvec x| where m∼T/T c near T c , in general agreement with the variational replica-symmetry breaking approach and with recent simulations of the disordered-substrate surface. For strong coupling the transition becomes first order

  5. Protein dynamics of human RPA and RAD51 on ssDNA during assembly and disassembly of the RAD51 filament.

    Science.gov (United States)

    Ma, Chu Jian; Gibb, Bryan; Kwon, YoungHo; Sung, Patrick; Greene, Eric C

    2017-01-25

    Homologous recombination (HR) is a crucial pathway for double-stranded DNA break (DSB) repair. During the early stages of HR, the newly generated DSB ends are processed to yield long single-stranded DNA (ssDNA) overhangs, which are quickly bound by replication protein A (RPA). RPA is then replaced by the DNA recombinase Rad51, which forms extended helical filaments on the ssDNA. The resulting nucleoprotein filament, known as the presynaptic complex, is responsible for pairing the ssDNA with homologous double-stranded DNA (dsDNA), which serves as the template to guide DSB repair. Here, we use single-molecule imaging to visualize the interplay between human RPA (hRPA) and human RAD51 during presynaptic complex assembly and disassembly. We demonstrate that ssDNA-bound hRPA can undergo facilitated exchange, enabling hRPA to undergo rapid exchange between free and ssDNA-bound states only when free hRPA is present in solution. Our results also indicate that the presence of free hRPA inhibits RAD51 filament nucleation, but has a lesser impact upon filament elongation. This finding suggests that hRPA exerts important regulatory influence over RAD51 and may in turn affect the properties of the assembled RAD51 filament. These experiments provide an important basis for further investigations into the regulation of human presynaptic complex assembly. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. Calculations of the properties of superconducting alloys via the average T-matrix approximation

    International Nuclear Information System (INIS)

    Chatterjee, P.

    1980-01-01

    The theoretical formula of McMillan, modified via the multiple-scattering theory by Gomersall and Gyorffy, has been very successful in computing the electron-phonon coupling constant (lambda) and the transition temperature (Tsub(c)) of many superconducting elements and compounds. For disordered solids, such as substitutional alloys, however, this theory fails because of the breakdown of the translational symmetry used in the multiple-scattering theory. Under these conditions the problem can still be solved if the t-matrix is averaged in the random phase approximation (average T-matrix approximation). Gomersall and Gyorffy's expression is reformulated for lambda in the random phase approximation. This theory is applied to calculate lambda and Tsub(c) of the binary substitutional NbMo alloy system at different concentrations. The results appear to be in fair agreement with experiments. (author)

  7. Modulated Pade approximant

    International Nuclear Information System (INIS)

    Ginsburg, C.A.

    1980-01-01

    In many problems, a desired property A of a function f(x) is determined by the behaviour of f(x) approximately equal to g(x,A) as x→xsup(*). In this letter, a method for resuming the power series in x of f(x) and approximating A (modulated Pade approximant) is presented. This new approximant is an extension of a resumation method for f(x) in terms of rational functions. (author)

  8. Monitoring Replication Protein A (RPA) dynamics in homologous recombination through site-specific incorporation of non-canonical amino acids.

    Science.gov (United States)

    Pokhrel, Nilisha; Origanti, Sofia; Davenport, Eric Parker; Gandhi, Disha; Kaniecki, Kyle; Mehl, Ryan A; Greene, Eric C; Dockendorff, Chris; Antony, Edwin

    2017-09-19

    An essential coordinator of all DNA metabolic processes is Replication Protein A (RPA). RPA orchestrates these processes by binding to single-stranded DNA (ssDNA) and interacting with several other DNA binding proteins. Determining the real-time kinetics of single players such as RPA in the presence of multiple DNA processors to better understand the associated mechanistic events is technically challenging. To overcome this hurdle, we utilized non-canonical amino acids and bio-orthogonal chemistry to site-specifically incorporate a chemical fluorophore onto a single subunit of heterotrimeric RPA. Upon binding to ssDNA, this fluorescent RPA (RPAf) generates a quantifiable change in fluorescence, thus serving as a reporter of its dynamics on DNA in the presence of multiple other DNA binding proteins. Using RPAf, we describe the kinetics of facilitated self-exchange and exchange by Rad51 and mediator proteins during various stages in homologous recombination. RPAf is widely applicable to investigate its mechanism of action in processes such as DNA replication, repair and telomere maintenance. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. Interactive Roles of DNA Helicases and Translocases with the Single-Stranded DNA Binding Protein RPA in Nucleic Acid Metabolism.

    Science.gov (United States)

    Awate, Sanket; Brosh, Robert M

    2017-06-08

    Helicases and translocases use the energy of nucleoside triphosphate binding and hydrolysis to unwind/resolve structured nucleic acids or move along a single-stranded or double-stranded polynucleotide chain, respectively. These molecular motors facilitate a variety of transactions including replication, DNA repair, recombination, and transcription. A key partner of eukaryotic DNA helicases/translocases is the single-stranded DNA binding protein Replication Protein A (RPA). Biochemical, genetic, and cell biological assays have demonstrated that RPA interacts with these human molecular motors physically and functionally, and their association is enriched in cells undergoing replication stress. The roles of DNA helicases/translocases are orchestrated with RPA in pathways of nucleic acid metabolism. RPA stimulates helicase-catalyzed DNA unwinding, enlists translocases to sites of action, and modulates their activities in DNA repair, fork remodeling, checkpoint activation, and telomere maintenance. The dynamic interplay between DNA helicases/translocases and RPA is just beginning to be understood at the molecular and cellular levels, and there is still much to be learned, which may inform potential therapeutic strategies.

  10. Sparse approximation with bases

    CERN Document Server

    2015-01-01

    This book systematically presents recent fundamental results on greedy approximation with respect to bases. Motivated by numerous applications, the last decade has seen great successes in studying nonlinear sparse approximation. Recent findings have established that greedy-type algorithms are suitable methods of nonlinear approximation in both sparse approximation with respect to bases and sparse approximation with respect to redundant systems. These insights, combined with some previous fundamental results, form the basis for constructing the theory of greedy approximation. Taking into account the theoretical and practical demand for this kind of theory, the book systematically elaborates a theoretical framework for greedy approximation and its applications.  The book addresses the needs of researchers working in numerical mathematics, harmonic analysis, and functional analysis. It quickly takes the reader from classical results to the latest frontier, but is written at the level of a graduate course and do...

  11. Theoretical nuclear physics: Progress report, October 1, 1987--October 1, 1988

    International Nuclear Information System (INIS)

    Kunz, P.D.; Rost, E.

    1988-09-01

    This paper discusses the following topics: Formulation of Non- Spectral Dirac Random Phase Approximation (RPA); Description of Discrete Transitions Using the Non-Spectral Dirac RPA; Sum Rules in Dirac RPA; The Coulomb Response for Quasi-Elastic (e,e') in Dirac RPA; Galerkin Approach to Dirac Problem with Finite Basis Splines; Open-Shell Nuclei in a Relativistic Mean-Field Model; An Alternative Interaction for the Relativistic Love Franey Model; Relativistic Suppression Factors in (p,d) Reaction Calculations; Effects of Initial and Final State Interactions on the P/bar P/ → Λ/bar /Lambda// Reaction; and Deuteron Knockout in the (e,e'd) Reaction

  12. Application of the Remotely Piloted Aircraft (RPA) 'MASC' in Atmospheric Boundary Layer Research

    Science.gov (United States)

    Wildmann, Norman; Bange, Jens

    2014-05-01

    The remotely piloted aircraft (RPA) MASC (Multipurpose Airborne Sensor Carrier) was developed at the University of Tübingen in cooperation with the University of Stuttgart, University of Applied Sciences Ostwestfalen-Lippe and 'ROKE-Modelle'. Its purpose is the investigation of thermodynamic processes in the atmospheric boundary layer (ABL), including observations of temperature, humidity and wind profiles, as well as the measurement of turbulent heat, moisture and momentum fluxes. The aircraft is electrically powered, has a maximum wingspan of 3.40 m and a total weight of 5-8 kg, depending on battery- and payload. The standard meteorological payload consists of temperature sensors, a humidity sensor, a flow probe, an inertial measurement unit and a GNSS. In normal operation, the aircraft is automatically controlled by the ROCS (Research Onboard Computer System) autopilot to be able to fly predefined paths at constant altitude and airspeed. Since 2010 the system has been tested and improved intensively. In September 2012 first comparative tests could successfully be performed at the Lindenberg observatory of Germany's National Meteorological Service (DWD). In 2013, several campaigns were done with the system, including fundamental boundary layer research, wind energy meteorology and assistive measurements to aerosol investigations. The results of a series of morning transition experiments in summer 2013 will be presented to demonstrate the capabilities of the measurement system. On several convective days between May and September, vertical soundings were done to record the evolution of the ABL in the early morning, from about one hour after sunrise, until noon. In between the soundings, flight legs of up to 1 km length were performed to measure turbulent statistics and fluxes at a constant altitude. With the help of surface flux measurements of a sonic anemometer, methods of similarity theory could be applied to the RPA flux measurements to compare them to

  13. Approximate symmetries of Hamiltonians

    Science.gov (United States)

    Chubb, Christopher T.; Flammia, Steven T.

    2017-08-01

    We explore the relationship between approximate symmetries of a gapped Hamiltonian and the structure of its ground space. We start by considering approximate symmetry operators, defined as unitary operators whose commutators with the Hamiltonian have norms that are sufficiently small. We show that when approximate symmetry operators can be restricted to the ground space while approximately preserving certain mutual commutation relations. We generalize the Stone-von Neumann theorem to matrices that approximately satisfy the canonical (Heisenberg-Weyl-type) commutation relations and use this to show that approximate symmetry operators can certify the degeneracy of the ground space even though they only approximately form a group. Importantly, the notions of "approximate" and "small" are all independent of the dimension of the ambient Hilbert space and depend only on the degeneracy in the ground space. Our analysis additionally holds for any gapped band of sufficiently small width in the excited spectrum of the Hamiltonian, and we discuss applications of these ideas to topological quantum phases of matter and topological quantum error correcting codes. Finally, in our analysis, we also provide an exponential improvement upon bounds concerning the existence of shared approximate eigenvectors of approximately commuting operators under an added normality constraint, which may be of independent interest.

  14. Cubic scaling algorithms for RPA correlation using interpolative separable density fitting

    Science.gov (United States)

    Lu, Jianfeng; Thicke, Kyle

    2017-12-01

    We present a new cubic scaling algorithm for the calculation of the RPA correlation energy. Our scheme splits up the dependence between the occupied and virtual orbitals in χ0 by use of Cauchy's integral formula. This introduces an additional integral to be carried out, for which we provide a geometrically convergent quadrature rule. Our scheme also uses the newly developed Interpolative Separable Density Fitting algorithm to further reduce the computational cost in a way analogous to that of the Resolution of Identity method.

  15. The Nuclear Scissors Mode by Two Approaches (Wigner Function Moments Versus RPA)

    CERN Document Server

    Balbutsev, E B

    2004-01-01

    Two complementary methods to describe the collective motion, RPA and Wigner Function Moments (WFM) method, are compared on an example of a simple model - harmonic oscillator with quadrupole-quadrupole residual interaction. It is shown that they give identical formulae for eigenfrequencies and transition probabilities of all collective excitations of the model including the scissors mode, which is a subject of our especial attention. The normalization factor of the "synthetic" scissors state and its overlap with physical states are calculated analytically. The orthogonality of the spurious state to all physical states is proved rigorously.

  16. New Clasp Assembly for Distal Extension Removable Partial Dentures: The Reverse RPA Clasp.

    Science.gov (United States)

    Hakkoum, Mohammad Ayham

    2016-07-01

    Several clasp types are used in distal extension removable partial dentures. In some cases the terminal abutments have only distal retentive undercuts that can be occupied by bar clasps; however, bar clasps may be contraindicated with no suitable alternative. This article presents a reasonable solution by introducing a new clasp design as a modification to the well-known RPA clasp. The design includes a mesial rest, proximal plate, and buccal retentive arm arising from the rest and extending to reach the distal retentive undercut. © 2015 by the American College of Prosthodontists.

  17. Approximating distributions from moments

    Science.gov (United States)

    Pawula, R. F.

    1987-11-01

    A method based upon Pearson-type approximations from statistics is developed for approximating a symmetric probability density function from its moments. The extended Fokker-Planck equation for non-Markov processes is shown to be the underlying foundation for the approximations. The approximation is shown to be exact for the beta probability density function. The applicability of the general method is illustrated by numerous pithy examples from linear and nonlinear filtering of both Markov and non-Markov dichotomous noise. New approximations are given for the probability density function in two cases in which exact solutions are unavailable, those of (i) the filter-limiter-filter problem and (ii) second-order Butterworth filtering of the random telegraph signal. The approximate results are compared with previously published Monte Carlo simulations in these two cases.

  18. A translationally invariant RPA-calculation for 16O on the basis of an algebraic solution of the many-body oscillator problem

    International Nuclear Information System (INIS)

    Schwesinger, B.

    1978-01-01

    The solution of the many-body oscillator problem is used as a basis for a RPA-calculation of 16 O. The calculation is performed in a LS-coupling scheme with an interaction containing central, spin-orbit and tensor forces. The main differences with conventional RPA-calculations occur for the transition probabilities. (orig.) [de

  19. Wildlife-associated recreation trends in the United States: a technical document supporting the Forest Service 2010 RPA Assessment

    Science.gov (United States)

    Miranda H. Mockrin; Richard A. Aiken; Curtis H. Flather

    2012-01-01

    The Forest and Rangeland Renewable Resources Planning Act (RPA) of 1974 requires periodic assessments of the condition and trends of the Nation's renewable natural resources. In this report, we document recent and historical trends in hunting and wildlife watching to fulfill RPA requirements. Using data from the U.S. Department of the Interior, Fish and Wildlife...

  20. CONTRIBUTIONS TO RATIONAL APPROXIMATION,

    Science.gov (United States)

    Some of the key results of linear Chebyshev approximation theory are extended to generalized rational functions. Prominent among these is Haar’s...linear theorem which yields necessary and sufficient conditions for uniqueness. Some new results in the classic field of rational function Chebyshev...Furthermore a Weierstrass type theorem is proven for rational Chebyshev approximation. A characterization theorem for rational trigonometric Chebyshev approximation in terms of sign alternation is developed. (Author)

  1. Approximation techniques for engineers

    CERN Document Server

    Komzsik, Louis

    2006-01-01

    Presenting numerous examples, algorithms, and industrial applications, Approximation Techniques for Engineers is your complete guide to the major techniques used in modern engineering practice. Whether you need approximations for discrete data of continuous functions, or you''re looking for approximate solutions to engineering problems, everything you need is nestled between the covers of this book. Now you can benefit from Louis Komzsik''s years of industrial experience to gain a working knowledge of a vast array of approximation techniques through this complete and self-contained resource.

  2. Validation of the RTOG recursive partitioning analysis (RPA) classification for small-cell lung cancer-only brain metastases

    International Nuclear Information System (INIS)

    Videtic, Gregory M.M.; Adelstein, David J.; Mekhail, Tarek M.; Rice, Thomas W.; Stevens, Glen H.J.; Lee, S.-Y.; Suh, John H.

    2007-01-01

    Purpose: Radiation Therapy Oncology Group (RTOG) developed a prognostic classification based on a recursive partitioning analysis (RPA) of patient pretreatment characteristics from three completed brain metastases randomized trials. Clinical trials for patients with brain metastases generally exclude small-cell lung cancer (SCLC) cases. We hypothesize that the RPA classes are valid in the setting of SCLC brain metastases. Methods and Materials: A retrospective review of 154 SCLC patients with brain metastases treated between April 1983 and May 2005 was performed. RPA criteria used for class assignment were Karnofsky performance status (KPS), primary tumor status (PT), presence of extracranial metastases (ED), and age. Results: Median survival was 4.9 months, with 4 patients (2.6%) alive at analysis. Median follow-up was 4.7 months (range, 0.3-40.3 months). Median age was 65 (range, 42-85 years). Median KPS was 70 (range, 40-100). Number of patients with controlled PT and no ED was 20 (13%) and with ED, 27 (18%); without controlled PT and ED, 34 (22%) and with ED, 73 (47%). RPA class distribution was: Class I: 8 (5%); Class II: 96 (62%); Class III: 51 (33%). Median survivals (in months) by RPA class were: Class I: 8.6; Class II: 4.2; Class III: 2.3 (p = 0.0023). Conclusions: Survivals for SCLC-only brain metastases replicate the results from the RTOG RPA classification. These classes are therefore valid for brain metastases from SCLC, support the inclusion of SCLC patients in future brain metastases trials, and may also serve as a basis for historical comparisons

  3. Prognostic factors in brain metastases: should patients be selected for aggressive treatment according to recursive partitioning analysis (RPA) classes?

    International Nuclear Information System (INIS)

    Nieder, Carsten; Nestle, Ursula; Motaref, Babak; Walter, Karin; Niewald, Marcus; Schnabel, Klaus

    2000-01-01

    Purpose: To determine whether or not Radiation Therapy Oncology Group (RTOG) recursive partitioning analysis (RPA) derived prognostic classes for patients with brain metastases are generally applicable and can be recommended as rational strategy for patient selection for future clinical trials. Inclusion of time to non-CNS death as additional endpoint besides death from any cause might result in further valuable information, as survival limitation due to uncontrolled extracranial disease can be explored. Methods: We performed a retrospective analysis of prognostic factors for survival and time to non-CNS death in 528 patients treated at a single institution with radiotherapy or surgery plus radiotherapy for brain metastases. For this purpose, patients were divided into groups with Karnofsky performance status (KPS) 0.05 for RPA class II versus III). However, it was 8.5 months in RPA class II patients with controlled primary tumor, which was found to be the only prognostic factor for time to non-CNS death in patients with KPS ≥70%. In patients with KPS <70%, no statistically significant prognostic factors were identified for this endpoint. Conclusions: Despite some differences, this analysis essentially confirmed the value of RPA-derived prognostic classes, as published by the RTOG, when survival was chosen as endpoint. RPA class I patients seem to be most likely to profit from aggressive treatment strategies and should be included in appropriate clinical trials. However, their number appears to be very limited. Considering time to non-CNS death, our results suggest that certain patients in RPA class II also might benefit from increased local control of brain metastases

  4. S4S8-RPA phosphorylation as an indicator of cancer progression in oral squamous cell carcinomas.

    Science.gov (United States)

    Rector, Jeff; Kapil, Sasha; Treude, Kelly J; Kumm, Phyllis; Glanzer, Jason G; Byrne, Brendan M; Liu, Shengqin; Smith, Lynette M; DiMaio, Dominick J; Giannini, Peter; Smith, Russell B; Oakley, Greg G

    2017-02-07

    Oral cancers are easily accessible compared to many other cancers. Nevertheless, oral cancer is often diagnosed late, resulting in a poor prognosis. Most oral cancers are squamous cell carcinomas that predominantly develop from cell hyperplasias and dysplasias. DNA damage is induced in these tissues directly or indirectly in response to oncogene-induced deregulation of cellular proliferation. Consequently, a DNA Damage response (DDR) and a cell cycle checkpoint is activated. As dysplasia transitions to cancer, proteins involved in DNA damage and checkpoint signaling are mutated or silenced decreasing cell death while increasing genomic instability and allowing continued tumor progression. Hyperphosphorylation of Replication Protein A (RPA), including phosphorylation of Ser4 and Ser8 of RPA2, is a well-known indicator of DNA damage and checkpoint activation. In this study, we utilize S4S8-RPA phosphorylation as a marker for cancer development and progression in oral squamous cell carcinomas (OSCC). S4S8-RPA phosphorylation was observed to be low in normal cells, high in dysplasias, moderate in early grade tumors, and low in late stage tumors, essentially supporting the model of the DDR as an early barrier to tumorigenesis in certain types of cancers. In contrast, overall RPA expression was not correlative to DDR activation or tumor progression. Utilizing S4S8-RPA phosphorylation to indicate competent DDR activation in the future may have clinical significance in OSCC treatment decisions, by predicting the susceptibility of cancer cells to first-line platinum-based therapies for locally advanced, metastatic and recurrent OSCC.

  5. Expectation Consistent Approximate Inference

    DEFF Research Database (Denmark)

    Opper, Manfred; Winther, Ole

    2005-01-01

    We propose a novel framework for approximations to intractable probabilistic models which is based on a free energy formulation. The approximation can be understood from replacing an average over the original intractable distribution with a tractable one. It requires two tractable probability dis...

  6. Ordered cones and approximation

    CERN Document Server

    Keimel, Klaus

    1992-01-01

    This book presents a unified approach to Korovkin-type approximation theorems. It includes classical material on the approximation of real-valuedfunctions as well as recent and new results on set-valued functions and stochastic processes, and on weighted approximation. The results are notonly of qualitative nature, but include quantitative bounds on the order of approximation. The book is addressed to researchers in functional analysis and approximation theory as well as to those that want to applythese methods in other fields. It is largely self- contained, but the readershould have a solid background in abstract functional analysis. The unified approach is based on a new notion of locally convex ordered cones that are not embeddable in vector spaces but allow Hahn-Banach type separation and extension theorems. This concept seems to be of independent interest.

  7. RPA activates the XPF‐ERCC1 endonuclease to initiate processing of DNA interstrand crosslinks

    KAUST Repository

    Abdullah, Ummi B

    2017-06-13

    During replication‐coupled DNA interstrand crosslink (ICL) repair, the XPF‐ERCC1 endonuclease is required for the incisions that release, or “unhook”, ICLs, but the mechanism of ICL unhooking remains largely unknown. Incisions are triggered when the nascent leading strand of a replication fork strikes the ICL. Here, we report that while purified XPF‐ERCC1 incises simple ICL‐containing model replication fork structures, the presence of a nascent leading strand, modelling the effects of replication arrest, inhibits this activity. Strikingly, the addition of the single‐stranded DNA (ssDNA)‐binding replication protein A (RPA) selectively restores XPF‐ERCC1 endonuclease activity on this structure. The 5′–3′ exonuclease SNM1A can load from the XPF‐ERCC1‐RPA‐induced incisions and digest past the crosslink to quantitatively complete the unhooking reaction. We postulate that these collaborative activities of XPF‐ERCC1, RPA and SNM1A might explain how ICL unhooking is achieved in vivo.

  8. Mre11-Sae2 and RPA Collaborate to Prevent Palindromic Gene Amplification.

    Science.gov (United States)

    Deng, Sarah K; Yin, Yi; Petes, Thomas D; Symington, Lorraine S

    2015-11-05

    Foldback priming at DNA double-stranded breaks is one mechanism proposed to initiate palindromic gene amplification, a common feature of cancer cells. Here, we show that small (5-9 bp) inverted repeats drive the formation of large palindromic duplications, the major class of chromosomal rearrangements recovered from yeast cells lacking Sae2 or the Mre11 nuclease. RPA dysfunction increased the frequency of palindromic duplications in Sae2 or Mre11 nuclease-deficient cells by ∼ 1,000-fold, consistent with intra-strand annealing to create a hairpin-capped chromosome that is subsequently replicated to form a dicentric isochromosome. The palindromic duplications were frequently associated with duplication of a second chromosome region bounded by a repeated sequence and a telomere, suggesting the dicentric chromosome breaks and repairs by recombination between dispersed repeats to acquire a telomere. We propose secondary structures within single-stranded DNA are potent instigators of genome instability, and RPA and Mre11-Sae2 play important roles in preventing their formation and propagation, respectively. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. RPA activates the XPF‐ERCC1 endonuclease to initiate processing of DNA interstrand crosslinks

    KAUST Repository

    Abdullah, Ummi B; McGouran, Joanna F; Brolih, Sanja; Ptchelkine, Denis; El‐Sagheer, Afaf H; Brown, Tom; McHugh, Peter J

    2017-01-01

    During replication‐coupled DNA interstrand crosslink (ICL) repair, the XPF‐ERCC1 endonuclease is required for the incisions that release, or “unhook”, ICLs, but the mechanism of ICL unhooking remains largely unknown. Incisions are triggered when the nascent leading strand of a replication fork strikes the ICL. Here, we report that while purified XPF‐ERCC1 incises simple ICL‐containing model replication fork structures, the presence of a nascent leading strand, modelling the effects of replication arrest, inhibits this activity. Strikingly, the addition of the single‐stranded DNA (ssDNA)‐binding replication protein A (RPA) selectively restores XPF‐ERCC1 endonuclease activity on this structure. The 5′–3′ exonuclease SNM1A can load from the XPF‐ERCC1‐RPA‐induced incisions and digest past the crosslink to quantitatively complete the unhooking reaction. We postulate that these collaborative activities of XPF‐ERCC1, RPA and SNM1A might explain how ICL unhooking is achieved in vivo.

  10. Does quasi-long-range order in the two-dimensional XY model really survive weak random phase fluctuations?

    International Nuclear Information System (INIS)

    Mudry, Christopher; Wen Xiaogang

    1999-01-01

    Effective theories for random critical points are usually non-unitary, and thus may contain relevant operators with negative scaling dimensions. To study the consequences of the existence of negative-dimensional operators, we consider the random-bond XY model. It has been argued that the XY model on a square lattice, when weakly perturbed by random phases, has a quasi-long-range ordered phase (the random spin wave phase) at sufficiently low temperatures. We show that infinitely many relevant perturbations to the proposed critical action for the random spin wave phase were omitted in all previous treatments. The physical origin of these perturbations is intimately related to the existence of broadly distributed correlation functions. We find that those relevant perturbations do enter the Renormalization Group equations, and affect critical behavior. This raises the possibility that the random XY model has no quasi-long-range ordered phase and no Kosterlitz-Thouless (KT) phase transition

  11. Fractional Fourier domain optical image hiding using phase retrieval algorithm based on iterative nonlinear double random phase encoding.

    Science.gov (United States)

    Wang, Xiaogang; Chen, Wen; Chen, Xudong

    2014-09-22

    We present a novel image hiding method based on phase retrieval algorithm under the framework of nonlinear double random phase encoding in fractional Fourier domain. Two phase-only masks (POMs) are efficiently determined by using the phase retrieval algorithm, in which two cascaded phase-truncated fractional Fourier transforms (FrFTs) are involved. No undesired information disclosure, post-processing of the POMs or digital inverse computation appears in our proposed method. In order to achieve the reduction in key transmission, a modified image hiding method based on the modified phase retrieval algorithm and logistic map is further proposed in this paper, in which the fractional orders and the parameters with respect to the logistic map are regarded as encryption keys. Numerical results have demonstrated the feasibility and effectiveness of the proposed algorithms.

  12. Cryptanalysis and improvement of an optical image encryption scheme using a chaotic Baker map and double random phase encoding

    International Nuclear Information System (INIS)

    Chen, Jun-Xin; Fu, Chong; Zhu, Zhi-Liang; Zhang, Li-Bo; Zhang, Yushu

    2014-01-01

    In this paper, we evaluate the security of an enhanced double random phase encoding (DRPE) image encryption scheme (2013 J. Lightwave Technol. 31 2533). The original system employs a chaotic Baker map prior to DRPE to provide more protection to the plain image and hence promote the security level of DRPE, as claimed. However, cryptanalysis shows that this scheme is vulnerable to a chosen-plaintext attack, and the ciphertext can be precisely recovered. The corresponding improvement is subsequently reported upon the basic premise that no extra equipment or computational complexity is required. The simulation results and security analyses prove its effectiveness and security. The proposed achievements are suitable for all cryptosystems under permutation and, following that, the DRPE architecture, and we hope that our work can motivate the further research on optical image encryption. (paper)

  13. Cryptanalysis and improvement of an optical image encryption scheme using a chaotic Baker map and double random phase encoding

    Science.gov (United States)

    Chen, Jun-Xin; Zhu, Zhi-Liang; Fu, Chong; Zhang, Li-Bo; Zhang, Yushu

    2014-12-01

    In this paper, we evaluate the security of an enhanced double random phase encoding (DRPE) image encryption scheme (2013 J. Lightwave Technol. 31 2533). The original system employs a chaotic Baker map prior to DRPE to provide more protection to the plain image and hence promote the security level of DRPE, as claimed. However, cryptanalysis shows that this scheme is vulnerable to a chosen-plaintext attack, and the ciphertext can be precisely recovered. The corresponding improvement is subsequently reported upon the basic premise that no extra equipment or computational complexity is required. The simulation results and security analyses prove its effectiveness and security. The proposed achievements are suitable for all cryptosystems under permutation and, following that, the DRPE architecture, and we hope that our work can motivate the further research on optical image encryption.

  14. Information verification cryptosystem using one-time keys based on double random phase encoding and public-key cryptography

    Science.gov (United States)

    Zhao, Tieyu; Ran, Qiwen; Yuan, Lin; Chi, Yingying; Ma, Jing

    2016-08-01

    A novel image encryption system based on double random phase encoding (DRPE) and RSA public-key algorithm is proposed. The main characteristic of the system is that each encryption process produces a new decryption key (even for the same plaintext), thus the encryption system conforms to the feature of the one-time pad (OTP) cryptography. The other characteristic of the system is the use of fingerprint key. Only with the rightful authorization will the true decryption be obtained, otherwise the decryption will result in noisy images. So the proposed system can be used to determine whether the ciphertext is falsified by attackers. In addition, the system conforms to the basic agreement of asymmetric cryptosystem (ACS) due to the combination with the RSA public-key algorithm. The simulation results show that the encryption scheme has high robustness against the existing attacks.

  15. Optical image transformation and encryption by phase-retrieval-based double random-phase encoding and compressive ghost imaging

    Science.gov (United States)

    Yuan, Sheng; Yang, Yangrui; Liu, Xuemei; Zhou, Xin; Wei, Zhenzhuo

    2018-01-01

    An optical image transformation and encryption scheme is proposed based on double random-phase encoding (DRPE) and compressive ghost imaging (CGI) techniques. In this scheme, a secret image is first transformed into a binary image with the phase-retrieval-based DRPE technique, and then encoded by a series of random amplitude patterns according to the ghost imaging (GI) principle. Compressive sensing, corrosion and expansion operations are implemented to retrieve the secret image in the decryption process. This encryption scheme takes the advantage of complementary capabilities offered by the phase-retrieval-based DRPE and GI-based encryption techniques. That is the phase-retrieval-based DRPE is used to overcome the blurring defect of the decrypted image in the GI-based encryption, and the CGI not only reduces the data amount of the ciphertext, but also enhances the security of DRPE. Computer simulation results are presented to verify the performance of the proposed encryption scheme.

  16. Approximate and renormgroup symmetries

    Energy Technology Data Exchange (ETDEWEB)

    Ibragimov, Nail H. [Blekinge Institute of Technology, Karlskrona (Sweden). Dept. of Mathematics Science; Kovalev, Vladimir F. [Russian Academy of Sciences, Moscow (Russian Federation). Inst. of Mathematical Modeling

    2009-07-01

    ''Approximate and Renormgroup Symmetries'' deals with approximate transformation groups, symmetries of integro-differential equations and renormgroup symmetries. It includes a concise and self-contained introduction to basic concepts and methods of Lie group analysis, and provides an easy-to-follow introduction to the theory of approximate transformation groups and symmetries of integro-differential equations. The book is designed for specialists in nonlinear physics - mathematicians and non-mathematicians - interested in methods of applied group analysis for investigating nonlinear problems in physical science and engineering. (orig.)

  17. Approximate and renormgroup symmetries

    International Nuclear Information System (INIS)

    Ibragimov, Nail H.; Kovalev, Vladimir F.

    2009-01-01

    ''Approximate and Renormgroup Symmetries'' deals with approximate transformation groups, symmetries of integro-differential equations and renormgroup symmetries. It includes a concise and self-contained introduction to basic concepts and methods of Lie group analysis, and provides an easy-to-follow introduction to the theory of approximate transformation groups and symmetries of integro-differential equations. The book is designed for specialists in nonlinear physics - mathematicians and non-mathematicians - interested in methods of applied group analysis for investigating nonlinear problems in physical science and engineering. (orig.)

  18. Approximations of Fuzzy Systems

    Directory of Open Access Journals (Sweden)

    Vinai K. Singh

    2013-03-01

    Full Text Available A fuzzy system can uniformly approximate any real continuous function on a compact domain to any degree of accuracy. Such results can be viewed as an existence of optimal fuzzy systems. Li-Xin Wang discussed a similar problem using Gaussian membership function and Stone-Weierstrass Theorem. He established that fuzzy systems, with product inference, centroid defuzzification and Gaussian functions are capable of approximating any real continuous function on a compact set to arbitrary accuracy. In this paper we study a similar approximation problem by using exponential membership functions

  19. General Rytov approximation.

    Science.gov (United States)

    Potvin, Guy

    2015-10-01

    We examine how the Rytov approximation describing log-amplitude and phase fluctuations of a wave propagating through weak uniform turbulence can be generalized to the case of turbulence with a large-scale nonuniform component. We show how the large-scale refractive index field creates Fermat rays using the path integral formulation for paraxial propagation. We then show how the second-order derivatives of the Fermat ray action affect the Rytov approximation, and we discuss how a numerical algorithm would model the general Rytov approximation.

  20. Coherent-phase or random-phase acceleration of electron beams in solar flares

    Science.gov (United States)

    Aschwanden, Markus J.; Benz, Arnold O.; Montello, Maria L.

    1994-01-01

    Time structures of electron beam signatures at radio wavelengths are investigated to probe correlated versus random behavior in solar flares. In particular we address the issue whether acceleration and injection of electron beams is coherently modulated by a single source, or whether the injection is driven by a stochastic (possibly spatially fragmented) process. We analyze a total of approximately = 6000 type III bursts observed by Ikarus (Zurich) in the frequency range of 100-500 MHz, during 359 solar flares with simultaneous greater than or = 25 keV hard X-ray emission, in the years 1890-1983. In 155 flares we find a total of 260 continuous type III groups, with an average number of 13 +/- 9 bursts per group, a mean duration of D = 12 +/- 14 s, a mean period of P = 2.0 +/- 1.2 s, with the highest burst rate at a frequency of nu = 310 +/- 120 MHz. Pulse periods have been measured between 0.5 and 10 s, and can be described by an exponential distribution, i.e., N(P) varies as e (exp -P/1.0s). The period shows a frequency dependence of P(nu)=46(exp-0.6)(sub MHz)s for different flares, but is invariant during a particular flare. We measure the mean period P and its standard deviation sigma (sub p) in each type III group, and quantify the degree of periodicity (or phase-coherence) by the dimensionless parameter sigma (sub p)P. The representative sample of 260 type III burst groups shows a mean periodicity of sigma (sub p/P) = 0.37 +/- 0.12, while Monte Carlo simulations of an equivalent set of truly random time series show a distinctly different value of sigma (sub p)P = 0.93 +/- 0.26. This result indicates that the injection of electron beams is coherently modulated by a particle acceleration source which is either compact or has a global organization on a timescale of seconds, in contrast to an incoherent acceleration source, which is stochastic either in time or space. We discuss the constraints on the size of the acceleration region resulting from electron beam

  1. Geometric approximation algorithms

    CERN Document Server

    Har-Peled, Sariel

    2011-01-01

    Exact algorithms for dealing with geometric objects are complicated, hard to implement in practice, and slow. Over the last 20 years a theory of geometric approximation algorithms has emerged. These algorithms tend to be simple, fast, and more robust than their exact counterparts. This book is the first to cover geometric approximation algorithms in detail. In addition, more traditional computational geometry techniques that are widely used in developing such algorithms, like sampling, linear programming, etc., are also surveyed. Other topics covered include approximate nearest-neighbor search, shape approximation, coresets, dimension reduction, and embeddings. The topics covered are relatively independent and are supplemented by exercises. Close to 200 color figures are included in the text to illustrate proofs and ideas.

  2. INTOR cost approximation

    International Nuclear Information System (INIS)

    Knobloch, A.F.

    1980-01-01

    A simplified cost approximation for INTOR parameter sets in a narrow parameter range is shown. Plausible constraints permit the evaluation of the consequences of parameter variations on overall cost. (orig.) [de

  3. Approximation and Computation

    CERN Document Server

    Gautschi, Walter; Rassias, Themistocles M

    2011-01-01

    Approximation theory and numerical analysis are central to the creation of accurate computer simulations and mathematical models. Research in these areas can influence the computational techniques used in a variety of mathematical and computational sciences. This collection of contributed chapters, dedicated to renowned mathematician Gradimir V. Milovanovia, represent the recent work of experts in the fields of approximation theory and numerical analysis. These invited contributions describe new trends in these important areas of research including theoretic developments, new computational alg

  4. Approximate kernel competitive learning.

    Science.gov (United States)

    Wu, Jian-Sheng; Zheng, Wei-Shi; Lai, Jian-Huang

    2015-03-01

    Kernel competitive learning has been successfully used to achieve robust clustering. However, kernel competitive learning (KCL) is not scalable for large scale data processing, because (1) it has to calculate and store the full kernel matrix that is too large to be calculated and kept in the memory and (2) it cannot be computed in parallel. In this paper we develop a framework of approximate kernel competitive learning for processing large scale dataset. The proposed framework consists of two parts. First, it derives an approximate kernel competitive learning (AKCL), which learns kernel competitive learning in a subspace via sampling. We provide solid theoretical analysis on why the proposed approximation modelling would work for kernel competitive learning, and furthermore, we show that the computational complexity of AKCL is largely reduced. Second, we propose a pseudo-parallelled approximate kernel competitive learning (PAKCL) based on a set-based kernel competitive learning strategy, which overcomes the obstacle of using parallel programming in kernel competitive learning and significantly accelerates the approximate kernel competitive learning for large scale clustering. The empirical evaluation on publicly available datasets shows that the proposed AKCL and PAKCL can perform comparably as KCL, with a large reduction on computational cost. Also, the proposed methods achieve more effective clustering performance in terms of clustering precision against related approximate clustering approaches. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Structural Basis of Mec1-Ddc2-RPA Assembly and Activation on Single-Stranded DNA at Sites of Damage.

    Science.gov (United States)

    Deshpande, Ishan; Seeber, Andrew; Shimada, Kenji; Keusch, Jeremy J; Gut, Heinz; Gasser, Susan M

    2017-10-19

    Mec1-Ddc2 (ATR-ATRIP) is a key DNA-damage-sensing kinase that is recruited through the single-stranded (ss) DNA-binding replication protein A (RPA) to initiate the DNA damage checkpoint response. Activation of ATR-ATRIP in the absence of DNA damage is lethal. Therefore, it is important that damage-specific recruitment precedes kinase activation, which is achieved at least in part by Mec1-Ddc2 homodimerization. Here, we report a structural, biochemical, and functional characterization of the yeast Mec1-Ddc2-RPA assembly. High-resolution co-crystal structures of Ddc2-Rfa1 and Ddc2-Rfa1-t11 (K45E mutant) N termini and of the Ddc2 coiled-coil domain (CCD) provide insight into Mec1-Ddc2 homodimerization and damage-site targeting. Based on our structural and functional findings, we present a Mec1-Ddc2-RPA-ssDNA composite structural model. By way of validation, we show that RPA-dependent recruitment of Mec1-Ddc2 is crucial for maintaining its homodimeric state at ssDNA and that Ddc2's recruitment domain and CCD are important for Mec1-dependent survival of UV-light-induced DNA damage. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. Outlook to 2060 for world forests and forest industries: a technical document supporting the Forest Service 2010 RPA assessment

    Science.gov (United States)

    Joseph Buongiorno; Shushuai Zhu; Ronald Raunikar; Jeffrey P. Prestemon

    2012-01-01

    Four RPA scenarios corresponding with scenarios from the Third and Fourth Assessments of the Intergovernmental Panel on Climate Change were simulated with the Global Forest Products Model to project forest area, volume, products demand and supply, international trade, prices, and value added up to 2060 for Africa, Asia, Europe, North America, Oceania, South America,...

  7. Forest Service programs, authorities, and relationships: A technical document supporting the 2000 USDA Forest Service RPA Assessment

    Science.gov (United States)

    Ervin G. Schuster; Michael A. Krebs

    2003-01-01

    The Forest and Rangeland Renewable Resources Planning Act (RPA) of 1974, as amended, directs the Forest Service to prepare and update a renewable resources assessment that would include "a description of Forest Service programs and responsibilities , their interrelationships, and the relationship of these programs and responsibilities to public and private...

  8. Forest Resources of the United States, 2012: a technical document supporting the Forest Service 2010 update of the RPA Assessment

    Science.gov (United States)

    Sonja N. Oswalt; W. Brad Smith; Patrick D. Miles; Scott A. Pugh

    2014-01-01

    Forest resource statistics from the 2010 Resources Planning Act (RPA) Assessment were updated to provide current information on the Nation's forests as a baseline for the 2015 national assessment. Resource tables present estimates of forest area, volume, mortality, growth, removals, and timber products output in various ways, such as by ownership, region, or State...

  9. RNA-processing proteins regulate Mec1/ATR activation by promoting generation of RPA-coated ssDNA.

    Science.gov (United States)

    Manfrini, Nicola; Trovesi, Camilla; Wery, Maxime; Martina, Marina; Cesena, Daniele; Descrimes, Marc; Morillon, Antonin; d'Adda di Fagagna, Fabrizio; Longhese, Maria Pia

    2015-02-01

    Eukaryotic cells respond to DNA double-strand breaks (DSBs) by activating a checkpoint that depends on the protein kinases Tel1/ATM and Mec1/ATR. Mec1/ATR is activated by RPA-coated single-stranded DNA (ssDNA), which arises upon nucleolytic degradation (resection) of the DSB. Emerging evidences indicate that RNA-processing factors play critical, yet poorly understood, roles in genomic stability. Here, we provide evidence that the Saccharomyces cerevisiae RNA decay factors Xrn1, Rrp6 and Trf4 regulate Mec1/ATR activation by promoting generation of RPA-coated ssDNA. The lack of Xrn1 inhibits ssDNA generation at the DSB by preventing the loading of the MRX complex. By contrast, DSB resection is not affected in the absence of Rrp6 or Trf4, but their lack impairs the recruitment of RPA, and therefore of Mec1, to the DSB. Rrp6 and Trf4 inactivation affects neither Rad51/Rad52 association nor DSB repair by homologous recombination (HR), suggesting that full Mec1 activation requires higher amount of RPA-coated ssDNA than HR-mediated repair. Noteworthy, deep transcriptome analyses do not identify common misregulated gene expression that could explain the observed phenotypes. Our results provide a novel link between RNA processing and genome stability. © 2014 The Authors.

  10. Code-Switching to Know a TL Equivalent of an L1 Word: Request-Provision-Acknowledgement (RPA) Sequence

    Science.gov (United States)

    Lucero, Edgar

    2011-01-01

    This article focuses on the learner's use of Code-switching to learn the TL (Target Language) equivalent of an L1 word. The interactional pattern that this situation creates defines the Request-Provision-Acknowledgement (RPA) sequence. The article explains each of the turns of the sequence under the combination of the Ethnomethodological…

  11. RPA prevents G-rich structure formation at lagging-strand telomeres to allow maintenance of chromosome ends.

    Science.gov (United States)

    Audry, Julien; Maestroni, Laetitia; Delagoutte, Emmanuelle; Gauthier, Tiphaine; Nakamura, Toru M; Gachet, Yannick; Saintomé, Carole; Géli, Vincent; Coulon, Stéphane

    2015-07-14

    Replication protein A (RPA) is a highly conserved heterotrimeric single-stranded DNA-binding protein involved in DNA replication, recombination, and repair. In fission yeast, the Rpa1-D223Y mutation provokes telomere shortening. Here, we show that this mutation impairs lagging-strand telomere replication and leads to the accumulation of secondary structures and recruitment of the homologous recombination factor Rad52. The presence of these secondary DNA structures correlates with reduced association of shelterin subunits Pot1 and Ccq1 at telomeres. Strikingly, heterologous expression of the budding yeast Pif1 known to efficiently unwind G-quadruplex rescues all the telomeric defects of the D223Y cells. Furthermore, in vitro data show that the identical D to Y mutation in human RPA specifically affects its ability to bind G-quadruplex. We propose that RPA prevents the formation of G-quadruplex structures at lagging-strand telomeres to promote shelterin association and facilitate telomerase action at telomeres. © 2015 The Authors.

  12. The Molecular Basis of Double-Strand DNA Break Repair: The Critical Structure of the RAD52/RPA Complex

    National Research Council Canada - National Science Library

    Jackson, Dobra

    2001-01-01

    .... RAD52 has specific interactions with RAD51, RPA and DNA (1,2,3). The binding of RAD52 to ends of double-strand breaks has been found to be a key initiation step to DNA repair by homologous recombination...

  13. TDA and RPA pseudoscalar and vector solutions for the low energy regime of a motivated QCD Hamiltonian.

    Science.gov (United States)

    Yépez-Martínez, T.; Amor Quiroz, D. A.; Hess, P. O.; Civitarese, O.

    2017-07-01

    We present the low energy meson spectrum of a Coulomb gauge QCD motivated Hamiltonian for light and strange quarks. We have used the harmonic oscillator as a trial basis and performed a pre-diagonalization of the kinetic energy term in order to get an effective basis where quark and anti-quark degrees of freedom are defined. For the relevant interactions between quarks and anti-quarks, we have implemented a confining interaction between color sources, in order to account in an effective way for the gluonic degrees of freedom. The low energy meson spectrum is obtained from the implementation of the TDA and RPA many-body-methods. The physical states have been described as TDA and RPA collective states with a relatively good agreement. Particularly, the particle-hole correlations of the RPA ground state improve the RPA pion-like state (159.7 MeV) close to its physical value while the TDA one remains at a higher energy (269.2 MeV).

  14. Projecting county-level populations under three future scenarios: a technical document supporting the Forest Service 2010 RPA Assessment

    Science.gov (United States)

    Stanley J. Zarnoch; H. Ken Cordell; Carter J. Betz

    2010-01-01

    County-level population projections from 2010 to 2060 are developed under three national population growth scenarios for reporting in the 2010 Renewable Resources Planning Act (RPA) Assessment. These population growth scenarios are tied to global futures scenarios defined by the Intergovernmental Panel on Climate Change (IPCC), a program within the United Nations...

  15. The N-terminus of RPA large subunit and its spatial position are important for the 5'->3' resection of DNA double-strand breaks.

    Science.gov (United States)

    Tammaro, Margaret; Liao, Shuren; McCane, Jill; Yan, Hong

    2015-10-15

    The first step of homology-dependent repair of DNA double-strand breaks (DSBs) is the resection of the 5' strand to generate 3' ss-DNA. Of the two major nucleases responsible for resection, EXO1 has intrinsic 5'->3' directionality, but DNA2 does not. DNA2 acts with RecQ helicases such as the Werner syndrome protein (WRN) and the heterotrimeric eukaryotic ss-DNA binding protein RPA. We have found that the N-terminus of the RPA large subunit (RPA1N) interacts with both WRN and DNA2 and is essential for stimulating WRN's 3'->5' helicase activity and DNA2's 5'->3' ss-DNA exonuclease activity. A mutant RPA complex that lacks RPA1N is unable to support resection in Xenopus egg extracts and human cells. Furthermore, relocating RPA1N to the middle subunit but not to the small subunit causes severe defects in stimulating DNA2 and WRN and in supporting resection. Together, these findings suggest that RPA1N and its spatial position are critical for restricting the directionality of the WRN-DNA2 resection pathway. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. The N-terminus of RPA large subunit and its spatial position are important for the 5′->3′ resection of DNA double-strand breaks

    Science.gov (United States)

    Tammaro, Margaret; Liao, Shuren; McCane, Jill; Yan, Hong

    2015-01-01

    The first step of homology-dependent repair of DNA double-strand breaks (DSBs) is the resection of the 5′ strand to generate 3′ ss-DNA. Of the two major nucleases responsible for resection, EXO1 has intrinsic 5′->3′ directionality, but DNA2 does not. DNA2 acts with RecQ helicases such as the Werner syndrome protein (WRN) and the heterotrimeric eukaryotic ss-DNA binding protein RPA. We have found that the N-terminus of the RPA large subunit (RPA1N) interacts with both WRN and DNA2 and is essential for stimulating WRN's 3′->5′ helicase activity and DNA2's 5′->3′ ss-DNA exonuclease activity. A mutant RPA complex that lacks RPA1N is unable to support resection in Xenopus egg extracts and human cells. Furthermore, relocating RPA1N to the middle subunit but not to the small subunit causes severe defects in stimulating DNA2 and WRN and in supporting resection. Together, these findings suggest that RPA1N and its spatial position are critical for restricting the directionality of the WRN-DNA2 resection pathway. PMID:26227969

  17. PRP19 transforms into a sensor of RPA-ssDNA after DNA damage and drives ATR activation via a ubiquitin-mediated circuitry.

    Science.gov (United States)

    Maréchal, Alexandre; Li, Ju-Mei; Ji, Xiao Ye; Wu, Ching-Shyi; Yazinski, Stephanie A; Nguyen, Hai Dang; Liu, Shizhou; Jiménez, Amanda E; Jin, Jianping; Zou, Lee

    2014-01-23

    PRP19 is a ubiquitin ligase involved in pre-mRNA splicing and the DNA damage response (DDR). Although the role for PRP19 in splicing is well characterized, its role in the DDR remains elusive. Through a proteomic screen for proteins that interact with RPA-coated single-stranded DNA (RPA-ssDNA), we identified PRP19 as a sensor of DNA damage. PRP19 directly binds RPA and localizes to DNA damage sites via RPA, promoting RPA ubiquitylation in a DNA-damage-induced manner. PRP19 facilitates the accumulation of ATRIP, the regulatory partner of the ataxia telangiectasia mutated and Rad3-related (ATR) kinase, at DNA damage sites. Depletion of PRP19 compromised the phosphorylation of ATR substrates, recovery of stalled replication forks, and progression of replication forks on damaged DNA. Importantly, PRP19 mutants that cannot bind RPA or function as an E3 ligase failed to support the ATR response, revealing that PRP19 drives ATR activation by acting as an RPA-ssDNA-sensing ubiquitin ligase during the DDR. Copyright © 2014 Elsevier Inc. All rights reserved.

  18. On Covering Approximation Subspaces

    Directory of Open Access Journals (Sweden)

    Xun Ge

    2009-06-01

    Full Text Available Let (U';C' be a subspace of a covering approximation space (U;C and X⊂U'. In this paper, we show that and B'(X⊂B(X∩U'. Also, iff (U;C has Property Multiplication. Furthermore, some connections between outer (resp. inner definable subsets in (U;C and outer (resp. inner definable subsets in (U';C' are established. These results answer a question on covering approximation subspace posed by J. Li, and are helpful to obtain further applications of Pawlak rough set theory in pattern recognition and artificial intelligence.

  19. Estudio, ensamblaje, caracterización y ensayos de dos modelos reales de RPA

    OpenAIRE

    Matienzo Merodio, Joel Juliá; Olmedilla García, Alfonso

    2016-01-01

    Un dron o un RPA (del inglés, Remote Piloted Aircraft) es un vehículo aéreo no tripulado capaz de despegar, volar y aterrizar de forma autónoma, semiautónoma o manual, siempre con control remoto. Además, toda aeronave de estas características debe ser capaz de mantener un nivel de vuelo controlado y sostenido. A lo largo de los años, estos aparatos han ido evolución tanto en aplicaciones como en su estética y características físicas, siempre impulsado por los requerimientos militares en c...

  20. On Convex Quadratic Approximation

    NARCIS (Netherlands)

    den Hertog, D.; de Klerk, E.; Roos, J.

    2000-01-01

    In this paper we prove the counterintuitive result that the quadratic least squares approximation of a multivariate convex function in a finite set of points is not necessarily convex, even though it is convex for a univariate convex function. This result has many consequences both for the field of

  1. Prestack wavefield approximations

    KAUST Repository

    Alkhalifah, Tariq

    2013-01-01

    The double-square-root (DSR) relation offers a platform to perform prestack imaging using an extended single wavefield that honors the geometrical configuration between sources, receivers, and the image point, or in other words, prestack wavefields. Extrapolating such wavefields, nevertheless, suffers from limitations. Chief among them is the singularity associated with horizontally propagating waves. I have devised highly accurate approximations free of such singularities which are highly accurate. Specifically, I use Padé expansions with denominators given by a power series that is an order lower than that of the numerator, and thus, introduce a free variable to balance the series order and normalize the singularity. For the higher-order Padé approximation, the errors are negligible. Additional simplifications, like recasting the DSR formula as a function of scattering angle, allow for a singularity free form that is useful for constant-angle-gather imaging. A dynamic form of this DSR formula can be supported by kinematic evaluations of the scattering angle to provide efficient prestack wavefield construction. Applying a similar approximation to the dip angle yields an efficient 1D wave equation with the scattering and dip angles extracted from, for example, DSR ray tracing. Application to the complex Marmousi data set demonstrates that these approximations, although they may provide less than optimal results, allow for efficient and flexible implementations. © 2013 Society of Exploration Geophysicists.

  2. Approximating The DCM

    DEFF Research Database (Denmark)

    Madsen, Rasmus Elsborg

    2005-01-01

    The Dirichlet compound multinomial (DCM), which has recently been shown to be well suited for modeling for word burstiness in documents, is here investigated. A number of conceptual explanations that account for these recent results, are provided. An exponential family approximation of the DCM...

  3. Approximation by Cylinder Surfaces

    DEFF Research Database (Denmark)

    Randrup, Thomas

    1997-01-01

    We present a new method for approximation of a given surface by a cylinder surface. It is a constructive geometric method, leading to a monorail representation of the cylinder surface. By use of a weighted Gaussian image of the given surface, we determine a projection plane. In the orthogonal...

  4. Prestack wavefield approximations

    KAUST Repository

    Alkhalifah, Tariq

    2013-09-01

    The double-square-root (DSR) relation offers a platform to perform prestack imaging using an extended single wavefield that honors the geometrical configuration between sources, receivers, and the image point, or in other words, prestack wavefields. Extrapolating such wavefields, nevertheless, suffers from limitations. Chief among them is the singularity associated with horizontally propagating waves. I have devised highly accurate approximations free of such singularities which are highly accurate. Specifically, I use Padé expansions with denominators given by a power series that is an order lower than that of the numerator, and thus, introduce a free variable to balance the series order and normalize the singularity. For the higher-order Padé approximation, the errors are negligible. Additional simplifications, like recasting the DSR formula as a function of scattering angle, allow for a singularity free form that is useful for constant-angle-gather imaging. A dynamic form of this DSR formula can be supported by kinematic evaluations of the scattering angle to provide efficient prestack wavefield construction. Applying a similar approximation to the dip angle yields an efficient 1D wave equation with the scattering and dip angles extracted from, for example, DSR ray tracing. Application to the complex Marmousi data set demonstrates that these approximations, although they may provide less than optimal results, allow for efficient and flexible implementations. © 2013 Society of Exploration Geophysicists.

  5. Phase-Image Encryption Based on 3D-Lorenz Chaotic System and Double Random Phase Encoding

    Science.gov (United States)

    Sharma, Neha; Saini, Indu; Yadav, AK; Singh, Phool

    2017-12-01

    In this paper, an encryption scheme for phase-images based on 3D-Lorenz chaotic system in Fourier domain under the 4f optical system is presented. The encryption scheme uses a random amplitude mask in the spatial domain and a random phase mask in the frequency domain. Its inputs are phase-images, which are relatively more secure as compared to the intensity images because of non-linearity. The proposed scheme further derives its strength from the use of 3D-Lorenz transform in the frequency domain. Although the experimental setup for optical realization of the proposed scheme has been provided, the results presented here are based on simulations on MATLAB. It has been validated for grayscale images, and is found to be sensitive to the encryption parameters of the Lorenz system. The attacks analysis shows that the key-space is large enough to resist brute-force attack, and the scheme is also resistant to the noise and occlusion attacks. Statistical analysis and the analysis based on correlation distribution of adjacent pixels have been performed to test the efficacy of the encryption scheme. The results have indicated that the proposed encryption scheme possesses a high level of security.

  6. Using a short-pulse diffraction-limited laser beam to probe filamentation of a random phase plate smoothed beam

    International Nuclear Information System (INIS)

    Kline, J. L.; Montgomery, D. S.; Flippo, K. A.; Johnson, R. P.; Rose, H. A.; Shimada, T.; Williams, E. A.

    2008-01-01

    A short pulse (few picoseconds) laser probe provides high temporal resolution measurements to elucidate details of fast dynamic phenomena not observable with typical longer laser pulse probes and gated diagnostics. Such a short pulse laser probe (SPLP) has been used to measure filamentation of a random phase plate (RPP) smoothed laser beam in a gas-jet plasma. The plasma index of refraction due to driven density and temperature fluctuations by the RPP beam perturbs the phase front of a SPLP propagating at a 90 deg. angle with respect to the RPP interaction beam. The density and temperature fluctuations are quasistatic on the time scale of the SPLP (∼2 ps). The transmitted near-field intensity distribution from the SPLP provides a measure of the phase front perturbation. At low plasma densities, the transmitted intensity pattern is asymmetric with striations across the entire probe beam in the direction of the RPP smoothed beam. As the plasma density increases, the striations break up into smaller sizes along the direction of the RPP beam propagation. The breakup of the intensity pattern is consistent with self-focusing of the RPP smoothed interaction beam. Simulations of the experiment using the wave propagation code, PF3D, are in qualitative agreement demonstrating that the asymmetric striations can be attributed to the RPP driven density fluctuations. Quantification of the beam breakup measured by the transmitted SPLP could lead to a new method for measuring self-focusing of lasers in underdense plasmas.

  7. Active control on high-order coherence and statistic characterization on random phase fluctuation of two classical point sources.

    Science.gov (United States)

    Hong, Peilong; Li, Liming; Liu, Jianji; Zhang, Guoquan

    2016-03-29

    Young's double-slit or two-beam interference is of fundamental importance to understand various interference effects, in which the stationary phase difference between two beams plays the key role in the first-order coherence. Different from the case of first-order coherence, in the high-order optical coherence the statistic behavior of the optical phase will play the key role. In this article, by employing a fundamental interfering configuration with two classical point sources, we showed that the high- order optical coherence between two classical point sources can be actively designed by controlling the statistic behavior of the relative phase difference between two point sources. Synchronous position Nth-order subwavelength interference with an effective wavelength of λ/M was demonstrated, in which λ is the wavelength of point sources and M is an integer not larger than N. Interestingly, we found that the synchronous position Nth-order interference fringe fingerprints the statistic trace of random phase fluctuation of two classical point sources, therefore, it provides an effective way to characterize the statistic properties of phase fluctuation for incoherent light sources.

  8. An improved saddlepoint approximation.

    Science.gov (United States)

    Gillespie, Colin S; Renshaw, Eric

    2007-08-01

    Given a set of third- or higher-order moments, not only is the saddlepoint approximation the only realistic 'family-free' technique available for constructing an associated probability distribution, but it is 'optimal' in the sense that it is based on the highly efficient numerical method of steepest descents. However, it suffers from the problem of not always yielding full support, and whilst [S. Wang, General saddlepoint approximations in the bootstrap, Prob. Stat. Lett. 27 (1992) 61.] neat scaling approach provides a solution to this hurdle, it leads to potentially inaccurate and aberrant results. We therefore propose several new ways of surmounting such difficulties, including: extending the inversion of the cumulant generating function to second-order; selecting an appropriate probability structure for higher-order cumulants (the standard moment closure procedure takes them to be zero); and, making subtle changes to the target cumulants and then optimising via the simplex algorithm.

  9. Prestack traveltime approximations

    KAUST Repository

    Alkhalifah, Tariq Ali

    2011-01-01

    Most prestack traveltime relations we tend work with are based on homogeneous (or semi-homogenous, possibly effective) media approximations. This includes the multi-focusing or double square-root (DSR) and the common reflection stack (CRS) equations. Using the DSR equation, I analyze the associated eikonal form in the general source-receiver domain. Like its wave-equation counterpart, it suffers from a critical singularity for horizontally traveling waves. As a result, I derive expansion based solutions of this eikonal based on polynomial expansions in terms of the reflection and dip angles in a generally inhomogenous background medium. These approximate solutions are free of singularities and can be used to estimate travetimes for small to moderate offsets (or reflection angles) in a generally inhomogeneous medium. A Marmousi example demonstrates the usefulness of the approach. © 2011 Society of Exploration Geophysicists.

  10. Topology, calculus and approximation

    CERN Document Server

    Komornik, Vilmos

    2017-01-01

    Presenting basic results of topology, calculus of several variables, and approximation theory which are rarely treated in a single volume, this textbook includes several beautiful, but almost forgotten, classical theorems of Descartes, Erdős, Fejér, Stieltjes, and Turán. The exposition style of Topology, Calculus and Approximation follows the Hungarian mathematical tradition of Paul Erdős and others. In the first part, the classical results of Alexandroff, Cantor, Hausdorff, Helly, Peano, Radon, Tietze and Urysohn illustrate the theories of metric, topological and normed spaces. Following this, the general framework of normed spaces and Carathéodory's definition of the derivative are shown to simplify the statement and proof of various theorems in calculus and ordinary differential equations. The third and final part is devoted to interpolation, orthogonal polynomials, numerical integration, asymptotic expansions and the numerical solution of algebraic and differential equations. Students of both pure an...

  11. Approximate Bayesian recursive estimation

    Czech Academy of Sciences Publication Activity Database

    Kárný, Miroslav

    2014-01-01

    Roč. 285, č. 1 (2014), s. 100-111 ISSN 0020-0255 R&D Projects: GA ČR GA13-13502S Institutional support: RVO:67985556 Keywords : Approximate parameter estimation * Bayesian recursive estimation * Kullback–Leibler divergence * Forgetting Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 4.038, year: 2014 http://library.utia.cas.cz/separaty/2014/AS/karny-0425539.pdf

  12. Approximating Preemptive Stochastic Scheduling

    OpenAIRE

    Megow Nicole; Vredeveld Tjark

    2009-01-01

    We present constant approximative policies for preemptive stochastic scheduling. We derive policies with a guaranteed performance ratio of 2 for scheduling jobs with release dates on identical parallel machines subject to minimizing the sum of weighted completion times. Our policies as well as their analysis apply also to the recently introduced more general model of stochastic online scheduling. The performance guarantee we give matches the best result known for the corresponding determinist...

  13. Optimization and approximation

    CERN Document Server

    Pedregal, Pablo

    2017-01-01

    This book provides a basic, initial resource, introducing science and engineering students to the field of optimization. It covers three main areas: mathematical programming, calculus of variations and optimal control, highlighting the ideas and concepts and offering insights into the importance of optimality conditions in each area. It also systematically presents affordable approximation methods. Exercises at various levels have been included to support the learning process.

  14. Can Electron Propagator Methods Be Used To Improve Polarization Propagator Methods?

    DEFF Research Database (Denmark)

    Jensen, Hans Jørgen Aagaard

    2008-01-01

    Calculations of Rydberg excitation energies with the second-order polarization propagator approximation (SOPPA) often produce results which are more in error than the random phase approximation (RPA), which formally is the first-order model. This is obviously because of cancellation of errors...... at the RPA level. On the other hand, valence excitation energies behave as expected, and they are systematically improved in SOPPA compared to RPA. Note that a Rydberg series is related to one of the ionization thresholds of the molecule, and it is thus obvious that a good description of the ionization...

  15. Cyclic approximation to stasis

    Directory of Open Access Journals (Sweden)

    Stewart D. Johnson

    2009-06-01

    Full Text Available Neighborhoods of points in $mathbb{R}^n$ where a positive linear combination of $C^1$ vector fields sum to zero contain, generically, cyclic trajectories that switch between the vector fields. Such points are called stasis points, and the approximating switching cycle can be chosen so that the timing of the switches exactly matches the positive linear weighting. In the case of two vector fields, the stasis points form one-dimensional $C^1$ manifolds containing nearby families of two-cycles. The generic case of two flows in $mathbb{R}^3$ can be diffeomorphed to a standard form with cubic curves as trajectories.

  16. On the WKBJ approximation

    International Nuclear Information System (INIS)

    El Sawi, M.

    1983-07-01

    A simple approach employing properties of solutions of differential equations is adopted to derive an appropriate extension of the WKBJ method. Some of the earlier techniques that are commonly in use are unified, whereby the general approximate solution to a second-order homogeneous linear differential equation is presented in a standard form that is valid for all orders. In comparison to other methods, the present one is shown to be leading in the order of iteration, and thus possibly has the ability of accelerating the convergence of the solution. The method is also extended for the solution of inhomogeneous equations. (author)

  17. The relaxation time approximation

    International Nuclear Information System (INIS)

    Gairola, R.P.; Indu, B.D.

    1991-01-01

    A plausible approximation has been made to estimate the relaxation time from a knowledge of the transition probability of phonons from one state (r vector, q vector) to other state (r' vector, q' vector), as a result of collision. The relaxation time, thus obtained, shows a strong dependence on temperature and weak dependence on the wave vector. In view of this dependence, relaxation time has been expressed in terms of a temperature Taylor's series in the first Brillouin zone. Consequently, a simple model for estimating the thermal conductivity is suggested. the calculations become much easier than the Callaway model. (author). 14 refs

  18. Polynomial approximation on polytopes

    CERN Document Server

    Totik, Vilmos

    2014-01-01

    Polynomial approximation on convex polytopes in \\mathbf{R}^d is considered in uniform and L^p-norms. For an appropriate modulus of smoothness matching direct and converse estimates are proven. In the L^p-case so called strong direct and converse results are also verified. The equivalence of the moduli of smoothness with an appropriate K-functional follows as a consequence. The results solve a problem that was left open since the mid 1980s when some of the present findings were established for special, so-called simple polytopes.

  19. Finite elements and approximation

    CERN Document Server

    Zienkiewicz, O C

    2006-01-01

    A powerful tool for the approximate solution of differential equations, the finite element is extensively used in industry and research. This book offers students of engineering and physics a comprehensive view of the principles involved, with numerous illustrative examples and exercises.Starting with continuum boundary value problems and the need for numerical discretization, the text examines finite difference methods, weighted residual methods in the context of continuous trial functions, and piecewise defined trial functions and the finite element method. Additional topics include higher o

  20. Microscopic mean field approximation and beyond with the Gogny force

    Directory of Open Access Journals (Sweden)

    Péru S.

    2014-03-01

    Full Text Available Fully consistent axially-symmetric-deformed quasiparticle random phase approximation calculations have been performed with the D1S Gogny force. A brief review on the main results obtained in this approach is presented. After a reminder on the method and on the first results concerning giant resonances in deformed Mg and Si isotopes, the multipole responses up to octupole in the deformed and heavy nucleus 238U are discussed. In order to analyse soft dipole modes in exotic nuclei, the dipole responses have been studied in Ne isotopes and in N=16 isotopes, for which results are presented. In these nuclei, the QRPA results on the low lying 2+ states are compared to the 5-Dimensional Collective Hamiltonian ones.

  1. Real-time RPA assay for rapid detection and differentiation of wild-type pseudorabies and gE-deleted vaccine viruses.

    Science.gov (United States)

    Wang, Jianchang; Liu, Libing; Wang, Jinfeng; Pang, Xiaoyu; Yuan, Wanzhe

    2018-02-15

    The objective of this study was to develop a dual real-time recombinase polymerase amplification (RPA) assay using exo probes for the detection and differentiation of pseudorabies virus (PRV). Specific RPA primers and probes were designed for gB and gE genes of PRV within the conserved region of viral genome. The reaction process can be completed in 20 min at 39 °C. The dual real-time RPA assay performed in the single tube was capable of specific detecting and differentiating of the wild-type PRV and gE-deleted vaccine strains, without cross-reactions with other non-targeted pig viruses. The analytical sensitivity of the assay was 10 2 copies for gB and gE genes. The dual real-time RPA demonstrated a 100% diagnostic agreement with the real-time PCR on 4 PRV strains and 37 clinical samples. Through the linear regression analysis, the R 2 value of the real-time RPA and the real-time PCR for gB and gE was 0.983 and 0.992, respectively. The dual real-time RPA assay provides an alternative useful tool for rapid, simple, and reliable detection and differentiation of PRV, especially in remote and rural areas. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Systemic treatment after whole-brain radiotherapy may improve survival in RPA class II/III breast cancer patients with brain metastasis.

    Science.gov (United States)

    Zhang, Qian; Chen, Jian; Yu, Xiaoli; Ma, Jinli; Cai, Gang; Yang, Zhaozhi; Cao, Lu; Chen, Xingxing; Guo, Xiaomao; Chen, Jiayi

    2013-09-01

    Whole brain radiotherapy (WBRT) is the most widely used treatment for brain metastasis (BM), especially for patients with multiple intracranial lesions. The purpose of this study was to examine the efficacy of systemic treatments following WBRT in breast cancer patients with BM who had different clinical characteristics, based on the classification of the Radiation Therapy Oncology Group recursive partitioning analysis (RPA) and the breast cancer-specific Graded Prognostic Assessment (Breast-GPA). One hundred and one breast cancer patients with BM treated between 2006 and 2010 were analyzed. The median interval between breast cancer diagnosis and identification of BM in the triple-negative patients was shorter than in the luminal A subtype (26 vs. 36 months, respectively; P = 0.021). Univariate analysis indicated that age at BM diagnosis, Karnofsky performance status/recursive partitioning analysis (KPS/RPA) classes, number of BMs, primary tumor control, extracranial metastases and systemic treatment following WBRT were significant prognostic factors for overall survival (OS) (P RPA classes and systemic treatments following WBRT remained the significant prognostic factors for OS. For RPA class I, the median survival with and without systemic treatments following WBRT was 25 and 22 months, respectively (P = 0.819), while for RPA class II/III systemic treatments significantly improved OS from 7 and 2 months to 11 and 5 months, respectively (P RPA class II/III patients.

  3. RPA accumulation during class switch recombination represents 5'-3' DNA-end resection during the S-G2/M phase of the cell cycle.

    Science.gov (United States)

    Yamane, Arito; Robbiani, Davide F; Resch, Wolfgang; Bothmer, Anne; Nakahashi, Hirotaka; Oliveira, Thiago; Rommel, Philipp C; Brown, Eric J; Nussenzweig, Andre; Nussenzweig, Michel C; Casellas, Rafael

    2013-01-31

    Activation-induced cytidine deaminase (AID) promotes chromosomal translocations by inducing DNA double-strand breaks (DSBs) at immunoglobulin (Ig) genes and oncogenes in the G1 phase. RPA is a single-stranded DNA (ssDNA)-binding protein that associates with resected DSBs in the S phase and facilitates the assembly of factors involved in homologous repair (HR), such as Rad51. Notably, RPA deposition also marks sites of AID-mediated damage, but its role in Ig gene recombination remains unclear. Here, we demonstrate that RPA associates asymmetrically with resected ssDNA in response to lesions created by AID, recombination-activating genes (RAG), or other nucleases. Small amounts of RPA are deposited at AID targets in G1 in an ATM-dependent manner. In contrast, recruitment in the S-G2/M phase is extensive, ATM independent, and associated with Rad51 accumulation. In the S-G2/M phase, RPA increases in nonhomologous-end-joining-deficient lymphocytes, where there is more extensive DNA-end resection. Thus, most RPA recruitment during class switch recombination represents salvage of unrepaired breaks by homology-based pathways during the S-G2/M phase of the cell cycle. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

  4. Approximate Bayesian computation.

    Directory of Open Access Journals (Sweden)

    Mikael Sunnåker

    Full Text Available Approximate Bayesian computation (ABC constitutes a class of computational methods rooted in Bayesian statistics. In all model-based statistical inference, the likelihood function is of central importance, since it expresses the probability of the observed data under a particular statistical model, and thus quantifies the support data lend to particular values of parameters and to choices among different models. For simple models, an analytical formula for the likelihood function can typically be derived. However, for more complex models, an analytical formula might be elusive or the likelihood function might be computationally very costly to evaluate. ABC methods bypass the evaluation of the likelihood function. In this way, ABC methods widen the realm of models for which statistical inference can be considered. ABC methods are mathematically well-founded, but they inevitably make assumptions and approximations whose impact needs to be carefully assessed. Furthermore, the wider application domain of ABC exacerbates the challenges of parameter estimation and model selection. ABC has rapidly gained popularity over the last years and in particular for the analysis of complex problems arising in biological sciences (e.g., in population genetics, ecology, epidemiology, and systems biology.

  5. Stereotactic ablative radiotherapy for comprehensive treatment of oligometastatic tumors (SABR-COMET): Study protocol for a randomized phase II trial

    International Nuclear Information System (INIS)

    Palma, David A; Griffioen, GwendolynHMJ; Gaede, Stewart; Slotman, Ben; Senan, Suresh; Haasbeek, Cornelis J A; Rodrigues, George B; Dahele, Max; Lock, Michael; Yaremko, Brian; Olson, Robert; Liu, Mitchell; Panarotto, Jason

    2012-01-01

    Stereotactic ablative radiotherapy (SABR) has emerged as a new treatment option for patients with oligometastatic disease. SABR delivers precise, high-dose, hypofractionated radiotherapy, and achieves excellent rates of local control. Survival outcomes for patients with oligometastatic disease treated with SABR appear promising, but conclusions are limited by patient selection, and the lack of adequate controls in most studies. The goal of this multicenter randomized phase II trial is to assess the impact of a comprehensive oligometastatic SABR treatment program on overall survival and quality of life in patients with up to 5 metastatic cancer lesions, compared to patients who receive standard of care treatment alone. After stratification by the number of metastases (1-3 vs. 4-5), patients will be randomized between Arm 1: current standard of care treatment, and Arm 2: standard of care treatment + SABR to all sites of known disease. Patients will be randomized in a 1:2 ratio to Arm 1:Arm 2, respectively. For patients receiving SABR, radiotherapy dose and fractionation depends on the site of metastasis and the proximity to critical normal structures. This study aims to accrue a total of 99 patients within four years. The primary endpoint is overall survival, and secondary endpoints include quality of life, toxicity, progression-free survival, lesion control rate, and number of cycles of further chemotherapy/systemic therapy. This study will provide an assessment of the impact of SABR on clinical outcomes and quality of life, to determine if long-term survival can be achieved for selected patients with oligometastatic disease, and will inform the design of a possible phase III study. Clinicaltrials.gov identifier: NCT01446744

  6. Cell-Free and In Vivo Characterization of Lux, Las, and Rpa Quorum Activation Systems in E. coli.

    Science.gov (United States)

    Halleran, Andrew D; Murray, Richard M

    2018-02-16

    Synthetic biologists have turned toward quorum systems as a path for building sophisticated microbial consortia that exhibit group decision making. Currently, however, even the most complex consortium circuits rely on only one or two quorum sensing systems, greatly restricting the available design space. High-throughput characterization of available quorum sensing systems is useful for finding compatible sets of systems that are suitable for a defined circuit architecture. Recently, cell-free systems have gained popularity as a test-bed for rapid prototyping of genetic circuitry. We take advantage of the transcription-translation cell-free system to characterize three commonly used Lux-type quorum activators, Lux, Las, and Rpa. We then compare the cell-free characterization to results obtained in vivo. We find significant genetic crosstalk in both the Las and Rpa systems and substantial signal crosstalk in Lux activation. We show that cell-free characterization predicts crosstalk observed in vivo.

  7. Caracterização da interação RPA-1-telômero em Trypanosoma cruzi.

    OpenAIRE

    Raphael Souza Pavani

    2014-01-01

    O complexo telomérico, responsável pela integridade genômica, é formado pela interação de DNA com proteínas, que são responsáveis pela proteção desses terminais. O complexo RPA de eucariotos compreende um heterotrímero, que cumpre diversas funções vitais na célula, sendo uma peça fundamental na replicação, reparo e recombinação. A ausência de homólogos de proteínas que protegem o telômero em T. cruzi nos fez investigar se o complexo RPA poderia cumprir essa função. Assim, este trabalho teve ...

  8. Ferromagnetism in diluted magnetic semiconductors: A comparision between AB INITIO mean-field, RPA, and Monte Carlo treatments

    Czech Academy of Sciences Publication Activity Database

    Bouzerar, G.; Kudrnovský, Josef; Bergqist, L.; Bruno, P.

    2003-01-01

    Roč. 68, č. 8 (2003), s. 081203-1 - 081203-4 ISSN 0163-1829 R&D Projects: GA AV ČR IAA1010203 Grant - others:RTN(XX) HPRN-CT-2000-00143 Institutional research plan: CEZ:AV0Z1010914 Keywords : Curie temperature * diluted magnetic semiconductors * mean-field * RPA * Monte-Carlo Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.962, year: 2003

  9. PILOTS NEEDED NCOS WELCOME: HOW ENLISTED RPA PILOTS CAN ENSURE AIR SUPERIORITY IN THE 21ST CENTURY

    Science.gov (United States)

    2016-06-01

    be used for the research. An analysis of the RPA manning problem will include operational tempo, retention , pilot shortage, outside job ... retention and recruitment would be higher. A recent article in a small business web site listed four major causes for job dissatisfaction: underpaid...9 High Operations Tempo……………………………………………………………...12 Job

  10. The quasilocalized charge approximation

    International Nuclear Information System (INIS)

    Kalman, G J; Golden, K I; Donko, Z; Hartmann, P

    2005-01-01

    The quasilocalized charge approximation (QLCA) has been used for some time as a formalism for the calculation of the dielectric response and for determining the collective mode dispersion in strongly coupled Coulomb and Yukawa liquids. The approach is based on a microscopic model in which the charges are quasilocalized on a short-time scale in local potential fluctuations. We review the conceptual basis and theoretical structure of the QLC approach and together with recent results from molecular dynamics simulations that corroborate and quantify the theoretical concepts. We also summarize the major applications of the QLCA to various physical systems, combined with the corresponding results of the molecular dynamics simulations and point out the general agreement and instances of disagreement between the two

  11. Differential RPA-1 and RAD-51 recruitment in vivo throughout the C. elegans germline, as revealed by laser microirradiation.

    Science.gov (United States)

    Koury, Emily; Harrell, Kailey; Smolikove, Sarit

    2018-01-25

    Studies of the repair pathways associated with DNA double strand breaks (DSBs) are numerous, and provide evidence for cell-cycle specific regulation of homologous recombination (HR) by the regulation of its associated proteins. Laser microirradiation is a well-established method to examine in vitro kinetics of repair and allows for live-imaging of DSB repair from the moment of induction. Here we apply this method to whole, live organisms, introducing an effective system to analyze exogenous, microirradiation-induced breaks in the Caenorhabditis elegans germline. Through this method we observed the sequential kinetics of the recruitment of ssDNA binding proteins RPA-1 and RAD-51 in vivo. We analyze these kinetics throughout different regions of the germline, and thus throughout a range of developmental stages of mitotic and meiotic nuclei. Our analysis demonstrates a largely conserved timing of recruitment of ssDNA binding proteins to DSBs throughout the germline, with a delay of RAD-51 recruitment at mid-pachytene nuclei. Microirradiated nuclei are viable and undergo a slow kinetics of resolution. We observe RPA-1 and RAD-51 colocalization for hours post-microirradiation throughout the germline, suggesting that there are mixed RPA-1/RAD-51 filaments. Finally, through live imaging analysis we observed RAD-51 foci movement with low frequency of coalescence. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Mean-Field and RPA Approaches to Stable and Unstable Nuclei with Semi-Realistic Interactions

    International Nuclear Information System (INIS)

    Nakada, H.

    2009-01-01

    We have developed semi-realistic NN interactions [1, 2] by modifying the M3Y interaction [3] that was derived from the G-matrix. The modification has been made so that the saturation and the spin-orbit splittings could be reproduced. The new interactions contain finite-range LS and tensor channels, as well as Yukawa-form central channels having reasonable spin and spin-isospin properties. In order to handle such interactions in practical calculations, we have also developed new numerical methods [4-6], in which the Gaussian expansion method [7] is applied. It is noted that these methods have the following advantages: (i) we can efficiently describe the energy-dependent asymptotics of single-particle wave functions at large r, as is typified in arguments on the deformed neutron halo in 4 0M g [6], (ii) we can handle various effective interactions, including those having non-locality, and (iii) a single-set of bases is applicable to wide mass range of nuclei and therefore is suitable to systematic calculations. Thereby we can implement Hartree-Fock, Hartree-Fock-Bogolyubov and RPA calculations for stable and unstable nuclei with the semi-realistic interactions. It will be shown first that the new interactions have desired characters for the nuclear matter and for the single- and double-closed nuclei. We shall particularly focus on roles of specific channels of the effective interaction, by studying (a) 'shell evolution' and role of the spin-isospin and the tensor channels [8] in stable and unstable nuclei, and (b) the magnetic response in a fully self-consistent RPA calculation with the tensor force [9]. All these properties seem to be simultaneously and naturally reproduced by the semi-realistic interactions. Thus the semi-realistic interactions are promising in describing various aspects of nuclear structure from stable to drip-line nuclei, in a self-consistent and unified manner. Since they have microscopic origin with minimal modification, we can expect high

  13. Approximate quantum Markov chains

    CERN Document Server

    Sutter, David

    2018-01-01

    This book is an introduction to quantum Markov chains and explains how this concept is connected to the question of how well a lost quantum mechanical system can be recovered from a correlated subsystem. To achieve this goal, we strengthen the data-processing inequality such that it reveals a statement about the reconstruction of lost information. The main difficulty in order to understand the behavior of quantum Markov chains arises from the fact that quantum mechanical operators do not commute in general. As a result we start by explaining two techniques of how to deal with non-commuting matrices: the spectral pinching method and complex interpolation theory. Once the reader is familiar with these techniques a novel inequality is presented that extends the celebrated Golden-Thompson inequality to arbitrarily many matrices. This inequality is the key ingredient in understanding approximate quantum Markov chains and it answers a question from matrix analysis that was open since 1973, i.e., if Lieb's triple ma...

  14. Prestack traveltime approximations

    KAUST Repository

    Alkhalifah, Tariq Ali

    2012-05-01

    Many of the explicit prestack traveltime relations used in practice are based on homogeneous (or semi-homogenous, possibly effective) media approximations. This includes the multifocusing, based on the double square-root (DSR) equation, and the common reflection stack (CRS) approaches. Using the DSR equation, I constructed the associated eikonal form in the general source-receiver domain. Like its wave-equation counterpart, it suffers from a critical singularity for horizontally traveling waves. As a result, I recasted the eikonal in terms of the reflection angle, and thus, derived expansion based solutions of this eikonal in terms of the difference between the source and receiver velocities in a generally inhomogenous background medium. The zero-order term solution, corresponding to ignoring the lateral velocity variation in estimating the prestack part, is free of singularities and can be used to estimate traveltimes for small to moderate offsets (or reflection angles) in a generally inhomogeneous medium. The higher-order terms include limitations for horizontally traveling waves, however, we can readily enforce stability constraints to avoid such singularities. In fact, another expansion over reflection angle can help us avoid these singularities by requiring the source and receiver velocities to be different. On the other hand, expansions in terms of reflection angles result in singularity free equations. For a homogenous background medium, as a test, the solutions are reasonably accurate to large reflection and dip angles. A Marmousi example demonstrated the usefulness and versatility of the formulation. © 2012 Society of Exploration Geophysicists.

  15. The UNG2 Arg88Cys variant abrogates RPA-mediated recruitment of UNG2 to single-stranded DNA.

    Science.gov (United States)

    Torseth, Kathrin; Doseth, Berit; Hagen, Lars; Olaisen, Camilla; Liabakk, Nina-Beate; Græsmann, Heidi; Durandy, Anne; Otterlei, Marit; Krokan, Hans E; Kavli, Bodil; Slupphaug, Geir

    2012-06-01

    In human cell nuclei, UNG2 is the major uracil-DNA glycosylase initiating DNA base excision repair of uracil. In activated B cells it has an additional role in facilitating mutagenic processing of AID-induced uracil at Ig loci and UNG-deficient patients develop hyper-IgM syndrome characterized by impaired class-switch recombination and disturbed somatic hypermutation. How UNG2 is recruited to either error-free or mutagenic uracil processing remains obscure, but likely involves regulated interactions with other proteins. The UNG2 N-terminal domain contains binding motifs for both proliferating cell nuclear antigen (PCNA) and replication protein A (RPA), but the relative contribution of these interactions to genomic uracil processing is not understood. Interestingly, a heterozygous germline single-nucleotide variant leading to Arg88Cys (R88C) substitution in the RPA-interaction motif of UNG2 has been observed in humans, but with unknown functional relevance. Here we demonstrate that UNG2-R88C protein is expressed from the variant allele in a lymphoblastoid cell line derived from a heterozygous germ line carrier. Enzyme activity as well as localization in replication foci of UNG2-R88C was similar to that of WT. However, binding to RPA was essentially abolished by the R88C substitution, whereas binding to PCNA was unaffected. Moreover, we show that disruption of the PCNA-binding motif impaired recruitment of UNG2 to S-phase replication foci, demonstrating that PCNA is a major factor for recruitment of UNG2 to unperturbed replication forks. Conversely, in cells treated with hydroxyurea, RPA mediated recruitment of UNG2 to stalled replication forks independently of functional PCNA binding. Modulation of PCNA- versus RPA-binding may thus constitute a functional switch for UNG2 in cells subsequent to genotoxic stress and potentially also during the processing of uracil at the immunoglobulin locus in antigen-stimulated B cells. Copyright © 2012 Elsevier B.V. All rights

  16. Efficacy and Safety of Axitinib Versus Sorafenib in Metastatic Renal Cell Carcinoma: Subgroup Analysis of Japanese Patients from the Global Randomized Phase 3 AXIS Trial

    OpenAIRE

    Ueda, Takeshi; Uemura, Hirotsugu; Tomita, Yoshihiko; Tsukamoto, Taiji; Kanayama, Hiroomi; Shinohara, Nobuo; Tarazi, Jamal; Chen, Connie; Kim, Sinil; Ozono, Seiichiro; Naito, Seiji; Akaza, Hideyuki

    2013-01-01

    Objective Axitinib is a potent and selective second-generation inhibitor of vascular endothelial growth factor receptors 1, 2 and 3. The efficacy and safety of axitinib in Japanese patients with metastatic renal cell carcinoma were evaluated. Methods A subgroup analysis was conducted in Japanese patients enrolled in the randomized Phase III trial of axitinib versus sorafenib after failure of one prior systemic therapy for metastatic renal cell carcinoma. Results Twenty-five (of 361) and 29 (o...

  17. Bond breaking and bond formation: how electron correlation is captured in many-body perturbation theory and density-functional theory.

    Science.gov (United States)

    Caruso, Fabio; Rohr, Daniel R; Hellgren, Maria; Ren, Xinguo; Rinke, Patrick; Rubio, Angel; Scheffler, Matthias

    2013-04-05

    For the paradigmatic case of H(2) dissociation, we compare state-of-the-art many-body perturbation theory in the GW approximation and density-functional theory in the exact-exchange plus random-phase approximation (RPA) for the correlation energy. For an unbiased comparison and to prevent spurious starting point effects, both approaches are iterated to full self-consistency (i.e., sc-RPA and sc-GW). The exchange-correlation diagrams in both approaches are topologically identical, but in sc-RPA they are evaluated with noninteracting and in sc-GW with interacting Green functions. This has a profound consequence for the dissociation region, where sc-RPA is superior to sc-GW. We argue that for a given diagrammatic expansion, sc-RPA outperforms sc-GW when it comes to bond breaking. We attribute this to the difference in the correlation energy rather than the treatment of the kinetic energy.

  18. Validation of the k-filtering technique for a signal composed of random-phase plane waves and non-random coherent structures

    Directory of Open Access Journals (Sweden)

    O. W. Roberts

    2014-12-01

    Full Text Available Recent observations of astrophysical magnetic fields have shown the presence of fluctuations being wave-like (propagating in the plasma frame and those described as being structure-like (advected by the plasma bulk velocity. Typically with single-spacecraft missions it is impossible to differentiate between these two fluctuations, due to the inherent spatio-temporal ambiguity associated with a single point measurement. However missions such as Cluster which contain multiple spacecraft have allowed for temporal and spatial changes to be resolved, using techniques such as k filtering. While this technique does not assume Taylor's hypothesis it requires both weak stationarity of the time series and that the fluctuations can be described by a superposition of plane waves with random phases. In this paper we test whether the method can cope with a synthetic signal which is composed of a combination of non-random-phase coherent structures with a mean radius d and a mean separation λ, as well as plane waves with random phase.

  19. A centrifugal direct recombinase polymerase amplification (direct-RPA) microdevice for multiplex and real-time identification of food poisoning bacteria.

    Science.gov (United States)

    Choi, Goro; Jung, Jae Hwan; Park, Byung Hyun; Oh, Seung Jun; Seo, Ji Hyun; Choi, Jong Seob; Kim, Do Hyun; Seo, Tae Seok

    2016-06-21

    In this study, we developed a centrifugal direct recombinase polymerase amplification (direct-RPA) microdevice for multiplex and real-time identification of food poisoning bacteria contaminated milk samples. The microdevice was designed to contain identical triplicate functional units and each unit has four reaction chambers, thereby making it possible to perform twelve direct-RPA reactions simultaneously. The integrated microdevice consisted of two layers: RPA reagents were injected in the top layer, while spiked milk samples with food poisoning bacteria were loaded into sample reservoirs in the bottom layer. For multiplex bacterial detection, the target gene-specific primers and probes were dried in each reaction chamber. The introduced samples and reagents could be equally aliquoted and dispensed into each reaction chamber by centrifugal force, and then the multiplex direct-RPA reaction was executed. The target genes of bacteria spiked in milk could be amplified at 39 °C without a DNA extraction step by using the direct-RPA cocktails, which were a combination of a direct PCR buffer and RPA enzymes. As the target gene amplification proceeded, the increased fluorescence signals coming from the reaction chambers were recorded in real-time at an interval of 2 min. The entire process, including the sample distribution, the direct-RPA reaction, and the real-time analysis, was accomplished with a custom-made portable genetic analyzer and a miniaturized optical detector. Monoplex, duplex, and triplex food poisoning bacteria (Salmonella enterica, Escherichia coli O157:H7, and Vibrio parahaemolyticus) detection was successfully performed with a detection sensitivity of 4 cells per 3.2 μL of milk samples within 30 min. By implementing the direct-PRA on the miniaturized centrifugal microsystem, the on-site food poisoning bacteria analysis would be feasible with high speed, sensitivity, and multiplicity.

  20. Self-similar factor approximants

    International Nuclear Information System (INIS)

    Gluzman, S.; Yukalov, V.I.; Sornette, D.

    2003-01-01

    The problem of reconstructing functions from their asymptotic expansions in powers of a small variable is addressed by deriving an improved type of approximants. The derivation is based on the self-similar approximation theory, which presents the passage from one approximant to another as the motion realized by a dynamical system with the property of group self-similarity. The derived approximants, because of their form, are called self-similar factor approximants. These complement the obtained earlier self-similar exponential approximants and self-similar root approximants. The specific feature of self-similar factor approximants is that their control functions, providing convergence of the computational algorithm, are completely defined from the accuracy-through-order conditions. These approximants contain the Pade approximants as a particular case, and in some limit they can be reduced to the self-similar exponential approximants previously introduced by two of us. It is proved that the self-similar factor approximants are able to reproduce exactly a wide class of functions, which include a variety of nonalgebraic functions. For other functions, not pertaining to this exactly reproducible class, the factor approximants provide very accurate approximations, whose accuracy surpasses significantly that of the most accurate Pade approximants. This is illustrated by a number of examples showing the generality and accuracy of the factor approximants even when conventional techniques meet serious difficulties

  1. Approximation for discrete Fourier transform and application in study of three-dimensional interacting electron gas.

    Science.gov (United States)

    Yan, Xin-Zhong

    2011-07-01

    The discrete Fourier transform is approximated by summing over part of the terms with corresponding weights. The approximation reduces significantly the requirement for computer memory storage and enhances the numerical computation efficiency with several orders without losing accuracy. As an example, we apply the algorithm to study the three-dimensional interacting electron gas under the renormalized-ring-diagram approximation where the Green's function needs to be self-consistently solved. We present the results for the chemical potential, compressibility, free energy, entropy, and specific heat of the system. The ground-state energy obtained by the present calculation is compared with the existing results of Monte Carlo simulation and random-phase approximation.

  2. The binding efficiency of RPA to telomeric G-strands folded into contiguous G-quadruplexes is independent of the number of G4 units.

    Science.gov (United States)

    Lancrey, Astrid; Safa, Layal; Chatain, Jean; Delagoutte, Emmanuelle; Riou, Jean-François; Alberti, Patrizia; Saintomé, Carole

    2018-03-01

    Replication protein A (RPA) is a single-stranded DNA binding protein involved in replication and in telomere maintenance. During telomere replication, G-quadruplexes (G4) can accumulate on the lagging strand template and need to be resolved. It has been shown that human RPA is able to unfold a single G4. Nevertheless, the G-strand of human telomeres is prone to fold into higher-order structures formed by contiguous G-quadruplexes. To understand how RPA deals with these structures, we studied its interaction with telomeric G-strands folding into an increasing number of contiguous G4s. The aim of this study was to determine whether the efficiency of binding/unfolding of hRPA to telomeric G-strands depends on the number of G4 units. Our data show that the number n of contiguous G4 units (n ≥ 2) does not affect the efficiency of hRPA to coat transiently exposed single-stranded telomeric G-strands. This feature may be essential in preventing instability due to G4 structures during telomere replication. Copyright © 2017 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  3. RFWD3-Mediated Ubiquitination Promotes Timely Removal of Both RPA and RAD51 from DNA Damage Sites to Facilitate Homologous Recombination.

    Science.gov (United States)

    Inano, Shojiro; Sato, Koichi; Katsuki, Yoko; Kobayashi, Wataru; Tanaka, Hiroki; Nakajima, Kazuhiro; Nakada, Shinichiro; Miyoshi, Hiroyuki; Knies, Kerstin; Takaori-Kondo, Akifumi; Schindler, Detlev; Ishiai, Masamichi; Kurumizaka, Hitoshi; Takata, Minoru

    2017-06-01

    RFWD3 is a recently identified Fanconi anemia protein FANCW whose E3 ligase activity toward RPA is essential in homologous recombination (HR) repair. However, how RPA ubiquitination promotes HR remained unknown. Here, we identified RAD51, the central HR protein, as another target of RFWD3. We show that RFWD3 polyubiquitinates both RPA and RAD51 in vitro and in vivo. Phosphorylation by ATR and ATM kinases is required for this activity in vivo. RFWD3 inhibits persistent mitomycin C (MMC)-induced RAD51 and RPA foci by promoting VCP/p97-mediated protein dynamics and subsequent degradation. Furthermore, MMC-induced chromatin loading of MCM8 and RAD54 is defective in cells with inactivated RFWD3 or expressing a ubiquitination-deficient mutant RAD51. Collectively, our data reveal a mechanism that facilitates timely removal of RPA and RAD51 from DNA damage sites, which is crucial for progression to the late-phase HR and suppression of the FA phenotype. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. International Conference Approximation Theory XV

    CERN Document Server

    Schumaker, Larry

    2017-01-01

    These proceedings are based on papers presented at the international conference Approximation Theory XV, which was held May 22–25, 2016 in San Antonio, Texas. The conference was the fifteenth in a series of meetings in Approximation Theory held at various locations in the United States, and was attended by 146 participants. The book contains longer survey papers by some of the invited speakers covering topics such as compressive sensing, isogeometric analysis, and scaling limits of polynomials and entire functions of exponential type. The book also includes papers on a variety of current topics in Approximation Theory drawn from areas such as advances in kernel approximation with applications, approximation theory and algebraic geometry, multivariate splines for applications, practical function approximation, approximation of PDEs, wavelets and framelets with applications, approximation theory in signal processing, compressive sensing, rational interpolation, spline approximation in isogeometric analysis, a...

  5. Hierarchical low-rank approximation for high dimensional approximation

    KAUST Repository

    Nouy, Anthony

    2016-01-01

    Tensor methods are among the most prominent tools for the numerical solution of high-dimensional problems where functions of multiple variables have to be approximated. Such high-dimensional approximation problems naturally arise in stochastic analysis and uncertainty quantification. In many practical situations, the approximation of high-dimensional functions is made computationally tractable by using rank-structured approximations. In this talk, we present algorithms for the approximation in hierarchical tensor format using statistical methods. Sparse representations in a given tensor format are obtained with adaptive or convex relaxation methods, with a selection of parameters using crossvalidation methods.

  6. Hierarchical low-rank approximation for high dimensional approximation

    KAUST Repository

    Nouy, Anthony

    2016-01-07

    Tensor methods are among the most prominent tools for the numerical solution of high-dimensional problems where functions of multiple variables have to be approximated. Such high-dimensional approximation problems naturally arise in stochastic analysis and uncertainty quantification. In many practical situations, the approximation of high-dimensional functions is made computationally tractable by using rank-structured approximations. In this talk, we present algorithms for the approximation in hierarchical tensor format using statistical methods. Sparse representations in a given tensor format are obtained with adaptive or convex relaxation methods, with a selection of parameters using crossvalidation methods.

  7. Forms of Approximate Radiation Transport

    CERN Document Server

    Brunner, G

    2002-01-01

    Photon radiation transport is described by the Boltzmann equation. Because this equation is difficult to solve, many different approximate forms have been implemented in computer codes. Several of the most common approximations are reviewed, and test problems illustrate the characteristics of each of the approximations. This document is designed as a tutorial so that code users can make an educated choice about which form of approximate radiation transport to use for their particular simulation.

  8. Magnetic Dimer Excitations in Cs3Cr2CI9 Studied by Neutron Scattering

    DEFF Research Database (Denmark)

    Leuenberger, Bruno; Güdel, Hans U.; Kjems, Jørgen

    1985-01-01

    The energy dispersion of the singlet-triplet dimer excitation in Cs3Cr2CI9h as been studied by inelastic neutron scattering (INS) at temperatures down to 1.3 K. The results can be accounted for by using a completely isotropic Heisenberg Hamiltonian in the random phase approximation (RPA). Only...

  9. Dynamic of Ising model with transverse field for two coupled sublattices in disordered phase

    International Nuclear Information System (INIS)

    Sa Motta, C.E.H. de.

    1984-02-01

    The dynamics of the two coupled sublattices tridimensional Ising model in a transverse field was studied by means of a continued fraction expansion for coupled operators. The static Correlation Functions necessary for studying the dynamics were calculated with the Green's Functions Method in the Random Phase Approximation (RPA). The spectral function was calculated in the region T c → . (Author) [pt

  10. Gamow-Teller Strength Distributions for Some Magic Nuclei

    Directory of Open Access Journals (Sweden)

    Necla ÇAKMAK

    2014-12-01

    Full Text Available The total Gamow-Teller strengths and their energy distributions for 96Zr, 96Sr, 54Ca, 28O, 24C and 14C have been obtained within the framework of Random Phase Approximation (RPA. The effective interaction potential has been described by considering the commutativity of the Gamow-Teller operator with the central part of the nuclear Hamiltonian.

  11. The nuclear response function

    International Nuclear Information System (INIS)

    Bertsch, G.F.

    1983-01-01

    These lectures present the theory of the nuclear response in the Random Phase Approximation (RPA). In the first lecture, various relations are derived between densities and currents which give rise to the well-known sum rules. Then RPA is derived via the time-dependent Hartree theory. The various formulations of RPA are shown: the configuration space representation, the coordinate space representation, the Landau theory of infinite systems and the RPA for separable interactions constrained by consistency. The remarkable success of RPA in describing the collective density oscillations of closed shell nuclei is illustrated with a few examples. In the final lecture, the σtau response is discussed with the application of simple theoretical considerations to the empirical data. Finally, we point out several problems which remain in the response theory. (author)

  12. Approximation by planar elastic curves

    DEFF Research Database (Denmark)

    Brander, David; Gravesen, Jens; Nørbjerg, Toke Bjerge

    2016-01-01

    We give an algorithm for approximating a given plane curve segment by a planar elastic curve. The method depends on an analytic representation of the space of elastic curve segments, together with a geometric method for obtaining a good initial guess for the approximating curve. A gradient......-driven optimization is then used to find the approximating elastic curve....

  13. The karyopherin Kap95 and the C-termini of Rfa1, Rfa2, and Rfa3 are necessary for efficient nuclear import of functional RPA complex proteins in Saccharomyces cerevisiae.

    Science.gov (United States)

    Belanger, Kenneth D; Griffith, Amanda L; Baker, Heather L; Hansen, Jeanne N; Kovacs, Laura A Simmons; Seconi, Justin S; Strine, Andrew C

    2011-09-01

    Nuclear protein import in eukaryotic cells is mediated by karyopherin proteins, which bind to specific nuclear localization signals on substrate proteins and transport them across the nuclear envelope and into the nucleus. Replication protein A (RPA) is a nuclear protein comprised of three subunits (termed Rfa1, Rfa2, and Rfa3 in Saccharomyces cerevisiae) that binds single-stranded DNA and is essential for DNA replication, recombination, and repair. RPA associates with two different karyopherins in yeast, Kap95, and Msn5/Kap142. However, it is unclear which of these karyopherins is responsible for RPA nuclear import. We have generated GFP fusion proteins with each of the RPA subunits and demonstrate that these Rfa-GFP chimeras are functional in yeast cells. The intracellular localization of the RPA proteins in live cells is similar in wild-type and msn5Δ deletion strains but becomes primarily cytoplasmic in cells lacking functional Kap95. Truncating the C-terminus of any of the RPA subunits results in mislocalization of the proteins to the cytoplasm and a loss of protein-protein interactions between the subunits. Our data indicate that Kap95 is likely the primary karyopherin responsible for RPA nuclear import in yeast and that the C-terminal regions of Rfa1, Rfa2, and Rfa3 are essential for efficient nucleocytoplasmic transport of each RPA subunit.

  14. Development of a recombinase polymerase amplification lateral flow dipstick (RPA-LFD) for the field diagnosis of caprine arthritis-encephalitis virus (CAEV) infection.

    Science.gov (United States)

    Tu, Po-An; Shiu, Jia-Shian; Lee, Shu-Hwae; Pang, Victor Fei; Wang, De-Chi; Wang, Pei-Hwa

    2017-05-01

    Caprine arthritis-encephalitis (CAE) in goats is a complex disease syndrome caused by a lentivirus. This persistent viral infection results in arthritis in adult goats and encephalitis in lambs. The prognosis for the encephalitic form is normally poor, and this form of the disease has caused substantial economic losses for goat farmers. Hence, a more efficient detection platform based on recombinase polymerase amplification (RPA) and a lateral flow dipstick (LFD) was developed in the present study for detecting the proviral DNA of caprine arthritis-encephalitis virus (CAEV). Under the optimal incubation conditions, specifically, 30min at 37°C for RPA followed by 5min at room temperature for LFD, the assay was found to be sensitive to a lower limit of 80pg of total DNA and 10 copies of plasmid DNA. Furthermore, there was no cross-reaction with other tested viruses, including goat pox virus and bovine leukemia virus. Given its simplicity and portability, this RPA-LFD protocol can serve as an alternative tool to ELISA for the primary screening of CAEV, one that is suitable for both laboratory and field application. When the RPA-LFD was applied in parallel with serological ELISA for the detection of CAEV in field samples, the RPA-LFD assay exhibited a higher sensitivity than the traditional method, and 82% of the 200 samples collected in Taiwan were found to be positive. To our knowledge, this is the first report providing evidence to support the use of an RPA-LFD assay as a specific and sensitive platform for detecting CAEV proviral DNA in goats in a faster manner, one that is also applicable for on-site utilization at farms and that should be useful in both eradication programs and epidemiological studies. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Exact constants in approximation theory

    CERN Document Server

    Korneichuk, N

    1991-01-01

    This book is intended as a self-contained introduction for non-specialists, or as a reference work for experts, to the particular area of approximation theory that is concerned with exact constants. The results apply mainly to extremal problems in approximation theory, which in turn are closely related to numerical analysis and optimization. The book encompasses a wide range of questions and problems: best approximation by polynomials and splines; linear approximation methods, such as spline-approximation; optimal reconstruction of functions and linear functionals. Many of the results are base

  16. International Conference Approximation Theory XIV

    CERN Document Server

    Schumaker, Larry

    2014-01-01

    This volume developed from papers presented at the international conference Approximation Theory XIV,  held April 7–10, 2013 in San Antonio, Texas. The proceedings contains surveys by invited speakers, covering topics such as splines on non-tensor-product meshes, Wachspress and mean value coordinates, curvelets and shearlets, barycentric interpolation, and polynomial approximation on spheres and balls. Other contributed papers address a variety of current topics in approximation theory, including eigenvalue sequences of positive integral operators, image registration, and support vector machines. This book will be of interest to mathematicians, engineers, and computer scientists working in approximation theory, computer-aided geometric design, numerical analysis, and related approximation areas.

  17. Gamow-Teller resonances and a separable approximation for Skyrme tensor interactions

    Directory of Open Access Journals (Sweden)

    Severyukhin A. P.

    2012-12-01

    Full Text Available A finite rank separable approximation for the quasiparticle random phase approximation (QRPA with Skyrme interactions is applied to study properties of the Gamow-Teller (GT resonances in the neutron-rich Cd isotopes. This approximation enables one to reduce considerably the dimension of matrix that must be diagonalized to perform QRPA calculations in a very large configuration space. Our results from the SGII Skyrme interaction with the tensor interactions and the density-dependent zero-range pairing interaction show that the GT distribution is noticeably modified when the tensor correlations are taken into account. In particular, for 130Cd the dominant peak is moved 3.6 MeV downward and 10% of the GT distribution is shifted to the high excitation energy region near E=50MeV.

  18. Extended Lipkin-type models with residual proton-neutron interaction

    International Nuclear Information System (INIS)

    Stoica, S.

    1999-01-01

    Extended Lipkin-Meshkov-Glick (LMG) models for testing the Random Phase Approximation (RPA) and proton-neutron Random Phase Approximation (pnRPA) methods are developed taking into account explicitly the proton and neutron degrees of freedom. First, an extended LMG model for testing RPA is developed. The proton and neutron Hamiltonians are taken to be of the LMG form and, in addition, a residual proton-neutron interaction is included. Exact solutions in a SU(2) x SU(2) basis as well as the RPA solutions for the energy spectrum of the model Hamiltonian are obtained. Then, the behaviour of the first collective excited state is studied as a function of the interaction parameters of the model using the exact and RPA methods. Secondly, an extended LMG model for testing pnRPA method is developed. Besides the proton and neutron single particle terms two types of residual proton-neutron interactions, one simulating a particle-particle and the other a particle-hole interaction, are included in the model Hamiltonian, so that the model is exactly solvable in an isospin SU(2) x SU(2) basis. The exact and pnRPA spectra of the model Hamiltonian are calculated as a function of the model parameters and compared to each other. Furthermore, charge-changing operators simulating a nuclear beta decay and their action on eigenfunctions of the model Hamiltonian are defined, and transition amplitude of them are calculated using exact and pnRPA wave functions. The best agreement between the exact RPA-type calculations for spectra and transitions, was obtained when the correlated RPA ground state, instead of the uncorrelated HF ground state was employed and when both kinds of residual interactions (i.e. like- and unlike-particle two-body interactions) are included in the model Hamiltonians. (author)

  19. Some results in Diophantine approximation

    DEFF Research Database (Denmark)

    Pedersen, Steffen Højris

    the basic concepts on which the papers build. Among other it introduces metric Diophantine approximation, Mahler’s approach on algebraic approximation, the Hausdorff measure, and properties of the formal Laurent series over Fq. The introduction ends with a discussion on Mahler’s problem when considered......This thesis consists of three papers in Diophantine approximation, a subbranch of number theory. Preceding these papers is an introduction to various aspects of Diophantine approximation and formal Laurent series over Fq and a summary of each of the three papers. The introduction introduces...

  20. Limitations of shallow nets approximation.

    Science.gov (United States)

    Lin, Shao-Bo

    2017-10-01

    In this paper, we aim at analyzing the approximation abilities of shallow networks in reproducing kernel Hilbert spaces (RKHSs). We prove that there is a probability measure such that the achievable lower bound for approximating by shallow nets can be realized for all functions in balls of reproducing kernel Hilbert space with high probability, which is different with the classical minimax approximation error estimates. This result together with the existing approximation results for deep nets shows the limitations for shallow nets and provides a theoretical explanation on why deep nets perform better than shallow nets. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Spherical Approximation on Unit Sphere

    Directory of Open Access Journals (Sweden)

    Eman Samir Bhaya

    2018-01-01

    Full Text Available In this paper we introduce a Jackson type theorem for functions in LP spaces on sphere And study on best approximation of  functions in  spaces defined on unit sphere. our central problem is to describe the approximation behavior of functions in    spaces for  by modulus of smoothness of functions.

  2. Approximate circuits for increased reliability

    Science.gov (United States)

    Hamlet, Jason R.; Mayo, Jackson R.

    2015-08-18

    Embodiments of the invention describe a Boolean circuit having a voter circuit and a plurality of approximate circuits each based, at least in part, on a reference circuit. The approximate circuits are each to generate one or more output signals based on values of received input signals. The voter circuit is to receive the one or more output signals generated by each of the approximate circuits, and is to output one or more signals corresponding to a majority value of the received signals. At least some of the approximate circuits are to generate an output value different than the reference circuit for one or more input signal values; however, for each possible input signal value, the majority values of the one or more output signals generated by the approximate circuits and received by the voter circuit correspond to output signal result values of the reference circuit.

  3. Population and harvest trends of big game and small game species: a technical document supporting the USDA Forest Service Interim Update of the 2000 RPA Assessment

    Science.gov (United States)

    Curtis H. Flather; Michael S. Knowles; Stephen J. Brady

    2009-01-01

    This technical document supports the Forest Service's requirement to assess the status of renewable natural resources as mandated by the Forest and Rangeland Renewable Resources Planning Act of 1974 (RPA). It updates past reports on national and regional trends in population and harvest estimates for species classified as big game and small game. The trends...

  4. Forecasts of county-level land uses under three future scenarios: a technical document supporting the Forest Service 2010 RPA Assessment

    Science.gov (United States)

    David N. Wear

    2011-01-01

    Accurately forecasting future forest conditions and the implications for ecosystem services depends on understanding land use dynamics. In support of the 2010 Renewable Resources Planning Act (RPA) Assessment, we forecast changes in land uses for the coterminous United States in response to three scenarios. Our land use models forecast urbanization in response to the...

  5. Recombinase polymerase amplification (RPA) of CaMV-35S promoter and nos terminator for rapid detection of genetically modified crops.

    Science.gov (United States)

    Xu, Chao; Li, Liang; Jin, Wujun; Wan, Yusong

    2014-10-10

    Recombinase polymerase amplification (RPA) is a novel isothermal DNA amplification and detection technology that enables the amplification of DNA within 30 min at a constant temperature of 37-42 °C by simulating in vivo DNA recombination. In this study, based on the regulatory sequence of the cauliflower mosaic virus 35S (CaMV-35S) promoter and the Agrobacterium tumefaciens nopaline synthase gene (nos) terminator, which are widely incorporated in genetically modified (GM) crops, we designed two sets of RPA primers and established a real-time RPA detection method for GM crop screening and detection. This method could reliably detect as few as 100 copies of the target molecule in a sample within 15-25 min. Furthermore, the real-time RPA detection method was successfully used to amplify and detect DNA from samples of four major GM crops (maize, rice, cotton, and soybean). With this novel amplification method, the test time was significantly shortened and the reaction process was simplified; thus, this method represents an effective approach to the rapid detection of GM crops.

  6. Yeast Srs2 Helicase Promotes Redistribution of Single-Stranded DNA-Bound RPA and Rad52 in Homologous Recombination Regulation

    Directory of Open Access Journals (Sweden)

    Luisina De Tullio

    2017-10-01

    Full Text Available Srs2 is a super-family 1 helicase that promotes genome stability by dismantling toxic DNA recombination intermediates. However, the mechanisms by which Srs2 remodels or resolves recombination intermediates remain poorly understood. Here, single-molecule imaging is used to visualize Srs2 in real time as it acts on single-stranded DNA (ssDNA bound by protein factors that function in recombination. We demonstrate that Srs2 is highly processive and translocates rapidly (∼170 nt per second in the 3′→5′ direction along ssDNA saturated with replication protein A (RPA. We show that RPA is evicted from DNA during the passage of Srs2. Remarkably, Srs2 also readily removes the recombination mediator Rad52 from RPA-ssDNA and, in doing so, promotes rapid redistribution of both Rad52 and RPA. These findings have important mechanistic implications for understanding how Srs2 and related nucleic acid motor proteins resolve potentially pathogenic nucleoprotein intermediates.

  7. Rapid diagnosis of Theileria annulata by recombinase polymerase amplification combined with a lateral flow strip (LF-RPA) in epidemic regions.

    Science.gov (United States)

    Yin, Fangyuan; Liu, Junlong; Liu, Aihong; Li, Youquan; Luo, Jianxun; Guan, Guiquan; Yin, Hong

    2017-04-15

    Rapid and accurate diagnosis of Theileria annulata infection contributes to the formulation of strategies to eradicate this parasite. A simple and efficient diagnostic tool, recombinase polymerase amplification (RPA) combined with a lateral flow (LF) strip, was used in detection of Theileria and compared to other methods that require expensive instruments and skilled personnel. Herein, we established and optimized an LF-RPA method to detect the cytochrome b gene of T. annulata mitochondrial DNA from experimentally infected and field-collected blood samples. This method has many unparalleled characteristics, including that it is rapid (clear detection in 5min at constant temperature), sensitive (the limitation of detection is at least 2pg genomic DNA), and specific (no cross-reaction with other piroplasms that infect cattle). The LF-RPA assay was evaluated via testing 17 field blood samples and comparing the results of that of a PCR, showing 100% agreement, which demonstrates the ability of the LF-RPA assay to detect T. annulata infections in small number of samples (n=17). Taken together, the results indicate that this method could be used as an ideal diagnostic tool for detecting T. annulata in endemic regions with limited to fewer and local resources and could also be a potential technique for the surveillance and control of blood protozoa. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Wildlife population and harvest trends in the United States: a technical document supporting the Forest Service 2010 RPA Assessment

    Science.gov (United States)

    Curtis H. Flather; Michael S. Knowles; Martin F. Jones; Carol Schilli

    2013-01-01

    The Forest and Rangeland Renewable Resources Planning Act (RPA) of 1974 requires periodic assessments of the condition and trends of the nation's renewable natural resources. Data from many sources were used to document recent historical trends in big game, small game, migratory game birds, furbearers, nongame, and imperiled species. Big game and waterfowl have...

  9. Yeast Srs2 Helicase Promotes Redistribution of Single-Stranded DNA-Bound RPA and Rad52 in Homologous Recombination Regulation.

    Science.gov (United States)

    De Tullio, Luisina; Kaniecki, Kyle; Kwon, Youngho; Crickard, J Brooks; Sung, Patrick; Greene, Eric C

    2017-10-17

    Srs2 is a super-family 1 helicase that promotes genome stability by dismantling toxic DNA recombination intermediates. However, the mechanisms by which Srs2 remodels or resolves recombination intermediates remain poorly understood. Here, single-molecule imaging is used to visualize Srs2 in real time as it acts on single-stranded DNA (ssDNA) bound by protein factors that function in recombination. We demonstrate that Srs2 is highly processive and translocates rapidly (∼170 nt per second) in the 3'→5' direction along ssDNA saturated with replication protein A (RPA). We show that RPA is evicted from DNA during the passage of Srs2. Remarkably, Srs2 also readily removes the recombination mediator Rad52 from RPA-ssDNA and, in doing so, promotes rapid redistribution of both Rad52 and RPA. These findings have important mechanistic implications for understanding how Srs2 and related nucleic acid motor proteins resolve potentially pathogenic nucleoprotein intermediates. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  10. Recombinase Polymerase Amplification (RPA of CaMV-35S Promoter and nos Terminator for Rapid Detection of Genetically Modified Crops

    Directory of Open Access Journals (Sweden)

    Chao Xu

    2014-10-01

    Full Text Available Recombinase polymerase amplification (RPA is a novel isothermal DNA amplification and detection technology that enables the amplification of DNA within 30 min at a constant temperature of 37–42 °C by simulating in vivo DNA recombination. In this study, based on the regulatory sequence of the cauliflower mosaic virus 35S (CaMV-35S promoter and the Agrobacterium tumefaciens nopaline synthase gene (nos terminator, which are widely incorporated in genetically modified (GM crops, we designed two sets of RPA primers and established a real-time RPA detection method for GM crop screening and detection. This method could reliably detect as few as 100 copies of the target molecule in a sample within 15–25 min. Furthermore, the real-time RPA detection method was successfully used to amplify and detect DNA from samples of four major GM crops (maize, rice, cotton, and soybean. With this novel amplification method, the test time was significantly shortened and the reaction process was simplified; thus, this method represents an effective approach to the rapid detection of GM crops.

  11. Human XPC-hHR23B interacts with XPA-RPA in the recognition of triplex-directed psoralen DNA interstrand crosslinks

    DEFF Research Database (Denmark)

    Thoma, Brian S; Wakasugi, Mitsuo; Christensen, Jesper

    2005-01-01

    (NER), XPA-RPA, recognizes DNA ICLs. We now report the use of triplex technology to direct a site-specific psoralen ICL to a target DNA substrate to determine whether the human global genome NER damage recognition complex, XPC-hHR23B, recognizes this lesion. Our results demonstrate that XPC-hHR23B...... recognizes psoralen ICLs, which have a structure fundamentally different from other lesions that XPC-hHR23B is known to bind, with high affinity and specificity. XPC-hHR23B and XPA-RPA protein complexes were also observed to bind psoralen ICLs simultaneously, demonstrating not only that psoralen ICLs...... are recognized by XPC-hHR23B alone, but also that XPA-RPA may interact cooperatively with XPC-hHR23B on damaged DNA, forming a multimeric complex. Since XPC-hHR23B and XPA-RPA participate in the recognition and verification of DNA damage, these results support the hypothesis that interplay between components...

  12. Projections of the U.S. timber supply and demand situation to 2050 : draft findings from the USDA Forest Service 2000 RPA Timber Assessment.

    Science.gov (United States)

    Richard Haynes; Darius Adams; Ralph Alig; David Brooks; Irene Durbak; James Howard; Peter Ince; David McKeever; John Mills; Ken Skog; Xiaoping. Zhou

    2001-01-01

    The Draft RPA Timber Assessment projects, over the next 50 years, the likelihood of increasing abundance of softwoods in the South and decreasing abundance of hardwoods in the South. These trends in supply, along with projected contributions from the North and West, imply U.S. consumption needs could be met without increasing net product imports and would not increase...

  13. A temporal importance-performance analysis of recreation attributes on national forests: a technical document supporting the Forest Service update of the 2010 RPA Assessment

    Science.gov (United States)

    Ashley E. Askew; J.M. Bowker; Donald B.K. English; Stanley J. Zarnoch; Gary T. Green

    2017-01-01

    The outdoor recreation component of the 2010 Resources Planning Act (RPA) Assessment provided projections and modeling of participation and intensity by activity. Results provided insight into the future of multiple outdoor recreation activities through projections of participation rates, numbers of participants, days per participant, and total activity days. These...

  14. Fish and other aquatic resource trends in the United States: a technical document supporting the Forest Service 2010 RPA Assessment

    Science.gov (United States)

    Andrew J. Loftus; Curtis H. Flather

    2012-01-01

    The Forest and Rangeland Renewable Resources Planning Act (RPA) of 1974 requires periodic assessments of the status and trends in the Nation's renewable natural resources including fish and other aquatic species and their habitats. Data from a number of sources are used to document trends in habitat quality, populations, resource use, and patterns of imperilment...

  15. Approximate Dynamic Programming: Combining Regional and Local State Following Approximations.

    Science.gov (United States)

    Deptula, Patryk; Rosenfeld, Joel A; Kamalapurkar, Rushikesh; Dixon, Warren E

    2018-06-01

    An infinite-horizon optimal regulation problem for a control-affine deterministic system is solved online using a local state following (StaF) kernel and a regional model-based reinforcement learning (R-MBRL) method to approximate the value function. Unlike traditional methods such as R-MBRL that aim to approximate the value function over a large compact set, the StaF kernel approach aims to approximate the value function in a local neighborhood of the state that travels within a compact set. In this paper, the value function is approximated using a state-dependent convex combination of the StaF-based and the R-MBRL-based approximations. As the state enters a neighborhood containing the origin, the value function transitions from being approximated by the StaF approach to the R-MBRL approach. Semiglobal uniformly ultimately bounded (SGUUB) convergence of the system states to the origin is established using a Lyapunov-based analysis. Simulation results are provided for two, three, six, and ten-state dynamical systems to demonstrate the scalability and performance of the developed method.

  16. Oral tetrahydrouridine and decitabine for non-cytotoxic epigenetic gene regulation in sickle cell disease: A randomized phase 1 study.

    Directory of Open Access Journals (Sweden)

    Robert Molokie

    2017-09-01

    Full Text Available Sickle cell disease (SCD, a congenital hemolytic anemia that exacts terrible global morbidity and mortality, is driven by polymerization of mutated sickle hemoglobin (HbS in red blood cells (RBCs. Fetal hemoglobin (HbF interferes with this polymerization, but HbF is epigenetically silenced from infancy onward by DNA methyltransferase 1 (DNMT1.To pharmacologically re-induce HbF by DNMT1 inhibition, this first-in-human clinical trial (NCT01685515 combined 2 small molecules-decitabine to deplete DNMT1 and tetrahydrouridine (THU to inhibit cytidine deaminase (CDA, the enzyme that otherwise rapidly deaminates/inactivates decitabine, severely limiting its half-life, tissue distribution, and oral bioavailability. Oral decitabine doses, administered after oral THU 10 mg/kg, were escalated from a very low starting level (0.01, 0.02, 0.04, 0.08, or 0.16 mg/kg to identify minimal doses active in depleting DNMT1 without cytotoxicity. Patients were SCD adults at risk of early death despite standard-of-care, randomized 3:2 to THU-decitabine versus placebo in 5 cohorts of 5 patients treated 2X/week for 8 weeks, with 4 weeks of follow-up. The primary endpoint was ≥ grade 3 non-hematologic toxicity. This endpoint was not triggered, and adverse events (AEs were not significantly different in THU-decitabine-versus placebo-treated patients. At the decitabine 0.16 mg/kg dose, plasma concentrations peaked at approximately 50 nM (Cmax and remained elevated for several hours. This dose decreased DNMT1 protein in peripheral blood mononuclear cells by >75% and repetitive element CpG methylation by approximately 10%, and increased HbF by 4%-9% (P < 0.001, doubling fetal hemoglobin-enriched red blood cells (F-cells up to approximately 80% of total RBCs. Total hemoglobin increased by 1.2-1.9 g/dL (P = 0.01 as reticulocytes simultaneously decreased; that is, better quality and efficiency of HbF-enriched erythropoiesis elevated hemoglobin using fewer reticulocytes. Also

  17. A randomized phase III study of accelerated hyperfractionation versus standard in patients with unresected brain metastases: a report of the radiation therapy oncology group (RTOG) 9104

    International Nuclear Information System (INIS)

    Murray, Kevin J.; Scott, Charles; Greenberg, Harvey M.; Emami, Bahman; Seider, Michael; Vora, Nayana L.; Olson, Craig; Whitton, Anthony; Movsas, Benjamin; Curran, Walter

    1997-01-01

    Purpose: To compare 1-year survival and acute toxicity rates between an accelerated hyperfractionated (AH) radiotherapy (1.6 Gy b.i.d.) to a total dose of 54.4 Gy vs. an accelerated fractionation (AF) of 30 Gy in 10 daily fractions in patients with unresected brain metastasis. Methods and Materials: The Radiation Therapy Oncology Group (RTOG) accrued 445 patients to a Phase III comparison of accelerated hyperfractionation vs. standard fractionation from 1991 through 1995. All patients had histologic proof of malignancy at the primary site. Brain metastasis were measurable by CT or MRI scan and all patients had a Karnofsky performance score (KPS) of at least 70 and a neurologic function classification of 1 or 2. For AH, 32 Gy in 20 fractions over 10 treatment days (1.6 Gy twice daily) was delivered to the whole brain. A boost of 22.4 Gy in 14 fractions was delivered to each lesion with a 2-cm margin. Results: The average age in both groups was 60 years; nearly two-thirds of all patients had lung primaries. Of the 429 eligible and analyzable patients, the median survival time was 4.5 months in both arms. The 1-year survival rate was 19% in the AF arm vs. 16% in the AH arm. No difference in median or 1-year survival was observed among patients with solitary metastasis between treatment arms. Recursive partitioning analysis (RPA) classes have previously been identified and patients with a KPS of 70 or more, a controlled primary tumor, less than 65 years of age, and brain metastases only (RPA class I), had a 1-year survival of 35% in the AF arm vs. 25% in the AH arm (p = 0.95). In a multivariate model, only age, KPS, extent of metastatic disease (intracranial metastases only vs. intra- and extracranial metastases), and status of primary (controlled vs. uncontrolled) were statistically significant (at p < 0.05). Treatment assignment was not statistically significant. Overall Grade III or IV toxicity was equivalent in both arms, and one fatal toxicity at 44 days secondary

  18. Phase I study of safety and immunogenicity of an Escherichia coli-derived recombinant protective antigen (rPA) vaccine to prevent anthrax in adults.

    Science.gov (United States)

    Brown, Bruce K; Cox, Josephine; Gillis, Anita; VanCott, Thomas C; Marovich, Mary; Milazzo, Mark; Antonille, Tanya Santelli; Wieczorek, Lindsay; McKee, Kelly T; Metcalfe, Karen; Mallory, Raburn M; Birx, Deborah; Polonis, Victoria R; Robb, Merlin L

    2010-11-05

    The fatal disease caused by Bacillus anthracis is preventable with a prophylactic vaccine. The currently available anthrax vaccine requires a lengthy immunization schedule, and simpler and more immunogenic options for protection against anthrax are a priority for development. In this report we describe a phase I clinical trial testing the safety and immunogenicity of an anthrax vaccine using recombinant Escherichia coli-derived, B. anthracis protective antigen (rPA). A total of 73 healthy adults ages 18-40 were enrolled and 67 received 2 injections separated by 4 weeks of either buffered saline placebo, or rPA formulated with or without 704 µg/ml Alhydrogel® adjuvant in increasing doses (5, 25, 50, 100 µg) of rPA. Participants were followed for one year and safety and immunologic data were assessed. Tenderness and warmth were the most common post-injection site reactions. No serious adverse events related to the vaccine were observed. The most robust humoral immune responses were observed in subjects receiving 50 µg of rPA formulated with Alhydrogel® with a geometric mean concentration of anti-rPA IgG antibodies of 283 µg/ml and a toxin neutralizing geometric 50% reciprocal geometric mean titer of 1061. The highest lymphoproliferative peak cellular response (median Lymphocyte Stimulation Index of 29) was observed in the group receiving 25 µg Alhydrogel®-formulated rPA. The vaccine was safe, well tolerated and stimulated a robust humoral and cellular response after two doses. ClinicalTrials.gov NCT00057525.

  19. The efficiency of Flory approximation

    International Nuclear Information System (INIS)

    Obukhov, S.P.

    1984-01-01

    The Flory approximation for the self-avoiding chain problem is compared with a conventional perturbation theory expansion. While in perturbation theory each term is averaged over the unperturbed set of configurations, the Flory approximation is equivalent to the perturbation theory with the averaging over the stretched set of configurations. This imposes restrictions on the integration domain in higher order terms and they can be treated self-consistently. The accuracy δν/ν of Flory approximation for self-avoiding chain problems is estimated to be 2-5% for 1 < d < 4. (orig.)

  20. Approximate Implicitization Using Linear Algebra

    Directory of Open Access Journals (Sweden)

    Oliver J. D. Barrowclough

    2012-01-01

    Full Text Available We consider a family of algorithms for approximate implicitization of rational parametric curves and surfaces. The main approximation tool in all of the approaches is the singular value decomposition, and they are therefore well suited to floating-point implementation in computer-aided geometric design (CAGD systems. We unify the approaches under the names of commonly known polynomial basis functions and consider various theoretical and practical aspects of the algorithms. We offer new methods for a least squares approach to approximate implicitization using orthogonal polynomials, which tend to be faster and more numerically stable than some existing algorithms. We propose several simple propositions relating the properties of the polynomial bases to their implicit approximation properties.

  1. Rollout sampling approximate policy iteration

    NARCIS (Netherlands)

    Dimitrakakis, C.; Lagoudakis, M.G.

    2008-01-01

    Several researchers have recently investigated the connection between reinforcement learning and classification. We are motivated by proposals of approximate policy iteration schemes without value functions, which focus on policy representation using classifiers and address policy learning as a

  2. Weighted approximation with varying weight

    CERN Document Server

    Totik, Vilmos

    1994-01-01

    A new construction is given for approximating a logarithmic potential by a discrete one. This yields a new approach to approximation with weighted polynomials of the form w"n"(" "= uppercase)P"n"(" "= uppercase). The new technique settles several open problems, and it leads to a simple proof for the strong asymptotics on some L p(uppercase) extremal problems on the real line with exponential weights, which, for the case p=2, are equivalent to power- type asymptotics for the leading coefficients of the corresponding orthogonal polynomials. The method is also modified toyield (in a sense) uniformly good approximation on the whole support. This allows one to deduce strong asymptotics in some L p(uppercase) extremal problems with varying weights. Applications are given, relating to fast decreasing polynomials, asymptotic behavior of orthogonal polynomials and multipoint Pade approximation. The approach is potential-theoretic, but the text is self-contained.

  3. Framework for sequential approximate optimization

    NARCIS (Netherlands)

    Jacobs, J.H.; Etman, L.F.P.; Keulen, van F.; Rooda, J.E.

    2004-01-01

    An object-oriented framework for Sequential Approximate Optimization (SAO) isproposed. The framework aims to provide an open environment for thespecification and implementation of SAO strategies. The framework is based onthe Python programming language and contains a toolbox of Python

  4. miR-30a can inhibit DNA replication by targeting RPA1 thus slowing cancer cell proliferation.

    Science.gov (United States)

    Zou, Zhenyou; Ni, Mengjie; Zhang, Jing; Chen, Yongfeng; Ma, Hongyu; Qian, Shihan; Tang, Longhua; Tang, Jiamei; Yao, Hailun; Zhao, Chengbin; Lu, Xiongwen; Sun, Hongyang; Qian, Jue; Mao, Xiaoting; Lu, Xulin; Liu, Qun; Zen, Juping; Wu, Hanbing; Bao, Zhaosheng; Lin, Shudan; Sheng, Hongyu; Li, Yunlong; Liang, Yong; Chen, Zhiqiang; Zong, Dan

    2016-07-15

    Cell proliferation was inhibited following forced over-expression of miR-30a in the ovary cancer cell line A2780DX5 and the gastric cancer cell line SGC7901R. Interestingly, miR-30a targets the DNA replication protein RPA1, hinders the replication of DNA and induces DNA fragmentation. Furthermore, ataxia telangiectasia mutated (ATM) and checkpoint kinase 2 (CHK2) were phosphorylated after DNA damage, which induced p53 expression, thus triggering the S-phase checkpoint, arresting cell cycle progression and ultimately initiating cancer cell apoptosis. Therefore, forced miR-30a over-expression in cancer cells can be a potential way to inhibit tumour development. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

  5. Heterogeneous asymmetric recombinase polymerase amplification (haRPA) for rapid hygiene control of large-volume water samples.

    Science.gov (United States)

    Elsäßer, Dennis; Ho, Johannes; Niessner, Reinhard; Tiehm, Andreas; Seidel, Michael

    2018-04-01

    Hygiene of drinking water is periodically controlled by cultivation and enumeration of indicator bacteria. Rapid and comprehensive measurements of emerging pathogens are of increasing interest to improve drinking water safety. In this study, the feasibility to detect bacteriophage PhiX174 as a potential indicator for virus contamination in large volumes of water is demonstrated. Three consecutive concentration methods (continuous ultrafiltration, monolithic adsorption filtration, and centrifugal ultrafiltration) were combined to concentrate phages stepwise from 1250 L drinking water into 1 mL. Heterogeneous asymmetric recombinase polymerase amplification (haRPA) is applied as rapid detection method. Field measurements were conducted to test the developed system for hygiene online monitoring under realistic conditions. We could show that this system allows the detection of artificial contaminations of bacteriophage PhiX174 in drinking water pipelines. Copyright © 2018 Elsevier Inc. All rights reserved.

  6. Nucleotide fluctuation of radiation-resistant Halobacterium sp. NRC-1 single-stranded DNA-binding protein (RPA) genes

    Science.gov (United States)

    Holden, Todd; Tremberger, G., Jr.; Cheung, E.; Subramaniam, R.; Gadura, N.; Schneider, P.; Sullivan, R.; Flamholz, A.; Lieberman, D.; Cheung, T. D.

    2009-08-01

    The Single-Stranded DNA-Binding Protein (RPA) Genes in gamma ray radiation-resistant halophilic archaeon Halobacterium sp. NRC-1 were analyzed in terms of their nucleotide fluctuations. In an ATCG sequence, each base was assigned a number equal to its atomic number. The resulting numerical sequence was the basis of the statistical analysis in this study. Fractal analysis using the Higuchi method gave fractal dimensions of 2.04 and 2.06 for the gene sequences VNG2160 and VNG2162, respectively. The 16S rRNA sequence has a fractal dimension of 1.99. The di-nucleotide Shannon entropy values were found to be negatively correlated with the observed fractal dimensions (R2~ 0.992, N=3). Inclusion of Deinococcus radiodurans Rad-A in the regression analysis decreases the R2 slightly to 0.98 (N=4). A third VNG2163 RPA gene of unknown function but with upregulation activity under irradiation was found to have a fractal dimension of 2.05 and a Shannon entropy of 3.77 bits. The above results are similar to those found in bacterial Deinococcus radiodurans and suggest that their high radiation resistance property would have favored selection of CG di-nucleotide pairs. The two transcription factors TbpD (VNG7114) and TfbA (VNG 2184) were also studied. Using VNG7114, VNG2184, and VNG2163; the regression analysis of fractal dimension versus Shannon entropy shows that R2 ~ 0.997 for N =3. The VNG2163 unknown function may be related to the pathways with transcriptions closely regulated to sequences VNG7114 and VNG2184.

  7. Precession mode on high-K configurations: non-collective axially-symmetric limit of wobbling motion

    International Nuclear Information System (INIS)

    Shimizu, Yoshifumi R; Matsuzaki, Masayuki; Matsuyanagi, Kenichi

    2006-01-01

    The precession mode, the rotational excitation built on the high-K isomeric state, in comparison with the recently identified wobbling mode has been studied. The random-phase-approximation (RPA) formalism, which has been developed for the nuclear wobbling motion, is invoked and the precession phonon is obtained by the non-collective axially symmetric limit of the formalism. The excitation energies and the electromagnetic properties of the precession bands in 178 W are calculated, and it is found that the results of RPA calculations well correspond to those of the rotor model; the correspondence can be understood by an adiabatic approximation to the RPA phonon. As a by-product, it is also found that the problem of too small out-of-band B(E2) in our previous RPA wobbling calculations can be solved by a suitable choice of the triaxial deformation which corresponds to the one used in the rotor model

  8. Nuclear Hartree-Fock approximation testing and other related approximations

    International Nuclear Information System (INIS)

    Cohenca, J.M.

    1970-01-01

    Hartree-Fock, and Tamm-Dancoff approximations are tested for angular momentum of even-even nuclei. Wave functions, energy levels and momenta are comparatively evaluated. Quadripole interactions are studied following the Elliott model. Results are applied to Ne 20 [pt

  9. Shearlets and Optimally Sparse Approximations

    DEFF Research Database (Denmark)

    Kutyniok, Gitta; Lemvig, Jakob; Lim, Wang-Q

    2012-01-01

    Multivariate functions are typically governed by anisotropic features such as edges in images or shock fronts in solutions of transport-dominated equations. One major goal both for the purpose of compression as well as for an efficient analysis is the provision of optimally sparse approximations...... optimally sparse approximations of this model class in 2D as well as 3D. Even more, in contrast to all other directional representation systems, a theory for compactly supported shearlet frames was derived which moreover also satisfy this optimality benchmark. This chapter shall serve as an introduction...... to and a survey about sparse approximations of cartoon-like images by band-limited and also compactly supported shearlet frames as well as a reference for the state-of-the-art of this research field....

  10. Diophantine approximation and Dirichlet series

    CERN Document Server

    Queffélec, Hervé

    2013-01-01

    This self-contained book will benefit beginners as well as researchers. It is devoted to Diophantine approximation, the analytic theory of Dirichlet series, and some connections between these two domains, which often occur through the Kronecker approximation theorem. Accordingly, the book is divided into seven chapters, the first three of which present tools from commutative harmonic analysis, including a sharp form of the uncertainty principle, ergodic theory and Diophantine approximation to be used in the sequel. A presentation of continued fraction expansions, including the mixing property of the Gauss map, is given. Chapters four and five present the general theory of Dirichlet series, with classes of examples connected to continued fractions, the famous Bohr point of view, and then the use of random Dirichlet series to produce non-trivial extremal examples, including sharp forms of the Bohnenblust-Hille theorem. Chapter six deals with Hardy-Dirichlet spaces, which are new and useful Banach spaces of anal...

  11. Approximations to camera sensor noise

    Science.gov (United States)

    Jin, Xiaodan; Hirakawa, Keigo

    2013-02-01

    Noise is present in all image sensor data. Poisson distribution is said to model the stochastic nature of the photon arrival process, while it is common to approximate readout/thermal noise by additive white Gaussian noise (AWGN). Other sources of signal-dependent noise such as Fano and quantization also contribute to the overall noise profile. Question remains, however, about how best to model the combined sensor noise. Though additive Gaussian noise with signal-dependent noise variance (SD-AWGN) and Poisson corruption are two widely used models to approximate the actual sensor noise distribution, the justification given to these types of models are based on limited evidence. The goal of this paper is to provide a more comprehensive characterization of random noise. We concluded by presenting concrete evidence that Poisson model is a better approximation to real camera model than SD-AWGN. We suggest further modification to Poisson that may improve the noise model.

  12. Rational approximations for tomographic reconstructions

    International Nuclear Information System (INIS)

    Reynolds, Matthew; Beylkin, Gregory; Monzón, Lucas

    2013-01-01

    We use optimal rational approximations of projection data collected in x-ray tomography to improve image resolution. Under the assumption that the object of interest is described by functions with jump discontinuities, for each projection we construct its rational approximation with a small (near optimal) number of terms for a given accuracy threshold. This allows us to augment the measured data, i.e., double the number of available samples in each projection or, equivalently, extend (double) the domain of their Fourier transform. We also develop a new, fast, polar coordinate Fourier domain algorithm which uses our nonlinear approximation of projection data in a natural way. Using augmented projections of the Shepp–Logan phantom, we provide a comparison between the new algorithm and the standard filtered back-projection algorithm. We demonstrate that the reconstructed image has improved resolution without additional artifacts near sharp transitions in the image. (paper)

  13. Approximation methods in probability theory

    CERN Document Server

    Čekanavičius, Vydas

    2016-01-01

    This book presents a wide range of well-known and less common methods used for estimating the accuracy of probabilistic approximations, including the Esseen type inversion formulas, the Stein method as well as the methods of convolutions and triangle function. Emphasising the correct usage of the methods presented, each step required for the proofs is examined in detail. As a result, this textbook provides valuable tools for proving approximation theorems. While Approximation Methods in Probability Theory will appeal to everyone interested in limit theorems of probability theory, the book is particularly aimed at graduate students who have completed a standard intermediate course in probability theory. Furthermore, experienced researchers wanting to enlarge their toolkit will also find this book useful.

  14. Approximate reasoning in physical systems

    International Nuclear Information System (INIS)

    Mutihac, R.

    1991-01-01

    The theory of fuzzy sets provides excellent ground to deal with fuzzy observations (uncertain or imprecise signals, wavelengths, temperatures,etc.) fuzzy functions (spectra and depth profiles) and fuzzy logic and approximate reasoning. First, the basic ideas of fuzzy set theory are briefly presented. Secondly, stress is put on application of simple fuzzy set operations for matching candidate reference spectra of a spectral library to an unknown sample spectrum (e.g. IR spectroscopy). Thirdly, approximate reasoning is applied to infer an unknown property from information available in a database (e.g. crystal systems). Finally, multi-dimensional fuzzy reasoning techniques are suggested. (Author)

  15. Face Recognition using Approximate Arithmetic

    DEFF Research Database (Denmark)

    Marso, Karol

    Face recognition is image processing technique which aims to identify human faces and found its use in various different fields for example in security. Throughout the years this field evolved and there are many approaches and many different algorithms which aim to make the face recognition as effective...... processing applications the results do not need to be completely precise and use of the approximate arithmetic can lead to reduction in terms of delay, space and power consumption. In this paper we examine possible use of approximate arithmetic in face recognition using Eigenfaces algorithm....

  16. Approximate Reanalysis in Topology Optimization

    DEFF Research Database (Denmark)

    Amir, Oded; Bendsøe, Martin P.; Sigmund, Ole

    2009-01-01

    In the nested approach to structural optimization, most of the computational effort is invested in the solution of the finite element analysis equations. In this study, the integration of an approximate reanalysis procedure into the framework of topology optimization of continuum structures...

  17. Approximate Matching of Hierarchial Data

    DEFF Research Database (Denmark)

    Augsten, Nikolaus

    -grams of a tree are all its subtrees of a particular shape. Intuitively, two trees are similar if they have many pq-grams in common. The pq-gram distance is an efficient and effective approximation of the tree edit distance. We analyze the properties of the pq-gram distance and compare it with the tree edit...

  18. Approximation of Surfaces by Cylinders

    DEFF Research Database (Denmark)

    Randrup, Thomas

    1998-01-01

    We present a new method for approximation of a given surface by a cylinder surface. It is a constructive geometric method, leading to a monorail representation of the cylinder surface. By use of a weighted Gaussian image of the given surface, we determine a projection plane. In the orthogonal...

  19. Approximation properties of haplotype tagging

    Directory of Open Access Journals (Sweden)

    Dreiseitl Stephan

    2006-01-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are locations at which the genomic sequences of population members differ. Since these differences are known to follow patterns, disease association studies are facilitated by identifying SNPs that allow the unique identification of such patterns. This process, known as haplotype tagging, is formulated as a combinatorial optimization problem and analyzed in terms of complexity and approximation properties. Results It is shown that the tagging problem is NP-hard but approximable within 1 + ln((n2 - n/2 for n haplotypes but not approximable within (1 - ε ln(n/2 for any ε > 0 unless NP ⊂ DTIME(nlog log n. A simple, very easily implementable algorithm that exhibits the above upper bound on solution quality is presented. This algorithm has running time O((2m - p + 1 ≤ O(m(n2 - n/2 where p ≤ min(n, m for n haplotypes of size m. As we show that the approximation bound is asymptotically tight, the algorithm presented is optimal with respect to this asymptotic bound. Conclusion The haplotype tagging problem is hard, but approachable with a fast, practical, and surprisingly simple algorithm that cannot be significantly improved upon on a single processor machine. Hence, significant improvement in computatational efforts expended can only be expected if the computational effort is distributed and done in parallel.

  20. All-Norm Approximation Algorithms

    NARCIS (Netherlands)

    Azar, Yossi; Epstein, Leah; Richter, Yossi; Woeginger, Gerhard J.; Penttonen, Martti; Meineche Schmidt, Erik

    2002-01-01

    A major drawback in optimization problems and in particular in scheduling problems is that for every measure there may be a different optimal solution. In many cases the various measures are different ℓ p norms. We address this problem by introducing the concept of an All-norm ρ-approximation