76,692 research outputs found
Dynamic removal of replication protein A by Dna2 facilitates primer cleavage during Okazaki fragment processing in Saccharomyces cerevisiae
Eukaryotic Okazaki fragments are initiated by an RNA/DNA primer, which is removed before the fragments are joined. Polymerase d displaces the primer into a flap for processing. Dna2 nuclease/helicase and flap endonuclease 1 (FEN1) are proposed to cleave the flap. The single-stranded DNA binding protein, replication protein A (RPA), governs cleavage activity. Flap-bound RPA inhibits FEN1. This necessitates cleavage by Dna2, which is stimulated by RPA. FEN1 then cuts the remaining RPA-free flap to create a nick for ligation. Cleavage by Dna2 requires that it enter the 5'-end and track down the flap. Since Dna2 cleaves the RPA-bound flap, we investigated the mechanism by which Dna2 accesses the protein-coated flap for cleavage. Using a nuclease-defective Dna2 mutant, we showed that just binding of Dna2 dissociates the flap-bound RPA. Facile dissociation is specific to substrates with a genuine flap, and will not occur with an RPA-coated single strand. We also compared the cleavage patterns of Dna2 with and without RPA to better define RPA stimulation of Dna2. Stimulation derived from removal of DNA folding in the flap. Apparently, coordinated with its dissociation, RPA relinquishes the flap to Dna2 for tracking in a way that does not allow flap structure to reform. We also found that RPA strand melting activity promotes excessive flap elongation, but it is suppressed by Dna2-promoted RPA dissociation. Overall, results indicate that Dna2 and RPA coordinate their functions for efficient flap cleavage and preparation for FEN1
BLM and RMI1 alleviate RPA inhibition of topoIIIα decatenase activity
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
Random phase approximation and its extension for the quantum O(2) anharmonic oscillator
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 RPA approximations 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 RPA approximations. 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-Bogoliubov equation. We draw a parallel between the two approaches.Comment: 26 pages, Latex file, no figur
Inhomogeneous Gutzwiller approximation with random phase fluctuations for the Hubbard model
We present a detailed study of the time-dependent Gutzwiller approximation
for the Hubbard model. The formalism, labelled GA+RPA, allows us to compute
random-phase approximation-like (RPA) fluctuations on top of the Gutzwiller
approximation (GA). No restrictions are imposed on the charge and spin
configurations which makes the method suitable for the calculation of linear
excitations around symmetry-broken solutions. Well-behaved sum rules are obeyed
as in the Hartree-Fock (HF) plus RPA approach. Analytical results for a
two-site model and numerical results for charge-charge and current-current
dynamical correlation functions in one and two dimensions are compared with
exact and HF+RPA results, supporting the much better performance of GA+RPA with
respect to conventional HF+RPA theory.Comment: 14 pages, 6 figure
Particle-particle and quasiparticle random phase approximations: Connections to coupled cluster theory
We establish a formal connection between the particle-particle (pp) random
phase approximation (RPA) and the ladder channel of the coupled cluster doubles
(CCD) equations. The relationship between RPA and CCD is best understood within
a Bogoliubov quasiparticle (qp) RPA formalism. This work is a follow-up to our
previous formal proof on the connection between particle-hole (ph) RPA and
ring-CCD. Whereas RPA is a quasibosonic approximation, CC theory is a correct
bosonization in the sense that the wavefunction and Hilbert space are exactly
fermionic. Coupled cluster theory achieves this goal by interacting the ph
(ring) and pp (ladder) diagrams via a third channel that we here call
"crossed-ring" whose presence allows for full fermionic antisymmetry.
Additionally, coupled cluster incorporates what we call "mosaic" terms which
can be absorbed into defining a new effective one-body Hamiltonian. The
inclusion of these mosaic terms seems to be quite important. The pp-RPA an d
qp-RPA equations are textbook material in nuclear structure physics but are
largely unknown in quantum chemistry, where particle number fluctuations and
Bogoliubov determinants are rarely used. We believe that the ideas and
connections discussed in this paper may help design improved ways of
incorporating RPA correlation into density functionals based on a CC
perspective
Random-phase approximation and its applications in computational chemistry and materials science
The random-phase approximation (RPA) as an approach for computing the
electronic correlation energy is reviewed. After a brief account of its basic
concept and historical development, the paper is devoted to the theoretical
formulations of RPA, and its applications to realistic systems. With several
illustrating applications, we discuss the implications of RPA for computational
chemistry and materials science. The computational cost of RPA is also
addressed which is critical for its widespread use in future applications. In
addition, current correction schemes going beyond RPA and directions of further
development will be discussed.Comment: 25 pages, 11 figures, published online in J. Mater. Sci. (2012
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