Orthogonal Polynomial Projectors for the Projector Augmented Wave Method of Electronic Structure Calculations

The projector augmented wave (PAW) method for electronic structure calculations developed by Blochl [Phys. Rev. B 50, 17 953 (1994)] has been very successfully used for density functional studies. It has the numerical advantages of pseudopotential techniques while retaining the physics of all-electron formalisms. We describe a method for generating the set of atom-centered projector and basis functions that are needed for the PAW method. This scheme chooses the shapes of the projector functions from a set of orthogonal polynomials multiplied by a localizing weight factor. Numerical benefits of the scheme result from having direct control of the shape of the projector functions and from the use of a simple repulsive local potential term to eliminate ‘‘ghost state’’ problems, which can plague calculations of this kind. Electronic density of states results are presented for the mineral powellite (CaMoO4)

Comparison of the Projector Augmented-Wave, Pseudopotential, and Linearized Augmented-Plane-Wave Formalisms for Density-Functional Calculations of Solids

The projector augmented-wave (PAW) method was developed by Blöchl as a method to accurately and efficiently calculate the electronic structure of materials within the framework of density-functional theory. It contains the numerical advantages of pseudopotential calculations while retaining the physics of all-electron calculations, including the correct nodal behavior of the valence-electron wave functions and the ability to include upper core states in addition to valence states in the self-consistent iterations. It uses many of the same ideas developed by Vanderbilt in his soft pseudopotential\u27\u27 formalism and in earlier work by Blöchl in his generalized separable potentials,\u27\u27 and has been successfully demonstrated for several interesting materials. We have developed a version of the PAW formalism for general use in structural and dynamical studies of materials. In the present paper, we investigate the accuracy of this implementation in comparison with corresponding results obtained using pseudopotential and linearized augmented-plane-wave (LAPW) codes. We present results of calculations for the cohesive energy, equilibrium lattice constant, and bulk modulus for several representative covalent, ionic, and metallic materials including diamond, silicon, SiC, CaF2, fcc Ca, and bcc V. With the exception of CaF2, for which core-electron polarization effects are important, the structural properties of these materials are represented equally well by the PAW, LAPW, and pseudopotential formalisms

FÖRSTER TRANSFER CALCULATIONS BASED ON CRYSTAL STRUCTURE DATA FROM Agmenellum quadruplicatum C-PHYCOCYANIN

Excitation energy transfer in C-phycocyanin is modeled using the Forster inductive resonance mechanism. Detailed calculations are carried out using coordinates and orientations of the chromophores derived from X-ray crystallographic studies of C-phycocyanin from two different species (Schirmer et al, J. Mol. Biol. 184, 257–277 (1985) and ibid., 188, 651-677 (1986)). Spectral overlap integrals are estimated from absorption and fluorescence spectra of C-phycocyanin of Mastigocladus laminosus and its separated subunits. Calculations are carried out for the β-subunit, αβ-monomer, (αβ)3-trimer and (αβ)0-hexamer species with the following chromophore assignments: β155 = 's’(sensitizer), β84 =‘f (fluorescer) and α84 =‘m’(intermediate):]:. The calculations show that excitation transfer relaxation occurs to 3=98% within 200 ps in nearly every case; however, the rates increase as much as 10-fold for the higher aggregates. Comparison with experimental data on fluorescence decay and depolarization kinetics from the literature shows qualitative agreement with these calculations. We conclude that Forster transfer is sufficient to account for all of the observed fluorescence properties of C-phycocyanin in aggregation states up to the hexamer and in the absence of linker polypeptides

PHOTOCHEMISTRY OF PHYCOBILIPROTEINS

Native PEC from the cyanobacterium, Mastigocladus laminosus, and its isolated α-subunit show photoreversibly photochromic reactions with difference-maxima around 502 and 570 nm in the spectral region of the α-84 phycoviolobilin chromophore. (b) Native PEC and its β-subunit show little if any reversible photochemistry in the 600–620 nm region, where the phycocyanobilin chromophores on the β-subunit absorb maximally, (c) Reversible photochemistry is retained in ureadenatured PEC at pH = 7.0 or pH ≤ 3. The difference maxima are shifted to 510 and 600 nm, and the amplitudes are decreased. An irreversible absorbance increase occurs around 670 nm (pH ≤ 3). (d) The amplitude of the reversible photoreaction difference spectrum is maximum in the presence of 4–5 M urea or 1 M KSCN, conditions known to dissociate phycobiliprotein aggregates into monomers. At the same time, the phycocyanobilin chromophore(s) are bleached irreversibly, (e) The amplitude becomes very small in high aggregates, e.g. in phycobilisomes. (f) In a reciprocal manner, the phototransformation of native PEC leads to a reversible shift of its aggregation equilibrium between trimer and monomer. The latter is favored by orange, the former by green light, (g) It is concluded that the phycoviolobilin chromophore of PEC is responsible for reversible photochemistry in PEC, and that there is not only an influence of aggregation state on photochemistry, but also vice versa an effect of the status of the chromophore on aggregation state. This could constitute a primary signal in the putative function as sensory pigment, either directly, or indirectly via the release of other polypeptides, via photodynamic effects, or the like

THERMAL DENATURATION OF MONOMERIC AND TRIMERIC PHYCOCYANINS STUDIED BY STATIC AND SPECTROSCOPY POLARIZED TIME-RESOLVED FLUORESCENCE

C-Phycocyanin (PC) and allophycocyanin (APC). as well as the a-subunit of PC. have been isolated from the blue-green alga (cyanobacterium). Spirulina platensis. The effects of partial thermal denaturation of PC and of its state of aggregation have been studied by ps time-resolved, polarized fluorescence spectroscopy. All measurements have been performed under low photon fluxes (< 10’ ’ photonsipulse x cm’) to minimize singlet-singlet annihilation processes. A complex decay is obtained under most conditions, which can be fitted satisfactorily with a bi-exponential (7’ = 70400 ps. T? = 1000-3000 ps) for both the isotropic and the polarized part, but with different intensities and time constants for the two decay curves. The data are interpreted in the frameworkof the model first developed by Teak and Dale (Biochern. J. 116, 161 (1970)], which divides the spectroscopically different chromophores in (predominantly) sensitizing (s) and fluorescing U, ones. If one assumes temperature dependent losses in the energy transfer from the s to the f and between f chromophores. both the biexponential nature of the isotropic fluorescence decay and the polarization data can be rationalized. In the isotropic emission (corresponding to the population of excited states) the short lifetime is related to the s-,f transfer. the longer one to the “free“ decay of the final acceptor(s) (= f). The polarized part is dominated by an extremely short decay time. which is related to s+f transfer, as well as to resonance transfer between the f-chromophores

Electro-Magnetic Nucleon Form Factors and their Spectral Functions in Soliton Models

It is demonstrated that in simple soliton models essential features of the electro-magnetic nucleon form factors observed over three orders of magnitude in momentum transfer $t$ are naturally reproduced. The analysis shows that three basic ingredients are required: an extended object, partial coupling to vector mesons, and relativistic recoil corrections. We use for the extended object the standard skyrmion, one vector meson propagator for both isospin channels, and the relativistic boost to the Breit frame. Continuation to timelike $t$ leads to quite stable results for the spectral functions in the regime from the 2- or 3-pion threshold to about two rho masses. Especially the onset of the continuous part of the spectral functions at threshold can be reliably determined and there are strong analogies to the results imposed on dispersion theoretic approaches by the unitarity constraint.Comment: 24 pages, (RevTeX), 5 PS-figures; Data points in fig.2 and corresponding references added. Final version, to be published in Z.Physik

Superconductivity induced by inter-band nesting in the three-dimensional honeycomb lattice

In order to study whether the inter-band nesting can favor superconductivity arising from electron-electron repulsion in a three-dimensional system, we have looked at the repulsive Hubbard model on a stack of honeycomb (i.e., non-Bravais) lattices with the FLEX method, partly motivated by the superconductivity observed in MgB2. By systematically changing the shape of Fermi surface with varied band filling n and the third-direction hopping, we have found that the pair scattering across the two-bands is indeed found to give rise to gap functions that change sign across the bands and behave as an s- or d-wave within each band. This implies (a) the electron repulsion can assist gapful pairing when a phonon-mechanism pairing exists, and (b) the electron repulsion alone, when strong enough, can give rise to a d-wave-like pairing, which should be, for a group-theoretic reason, a time-reversal broken d+id with point nodes in the gap

Consistent off-shell πNN\pi N N vertex and nucleon self-energy

We present a consistent calculation of half-off-shell form factors in the pion-nucleon vertex and the nucleon self-energy. Numerical results are presented. Near the on-shell point the pion-nucleon vertex is dominated by the pseudovector coupling, while at large nucleon invariant masses we find a sizable pseudoscalar admixture.Comment: 23 pages, 7 figures, REVTeX, submitted to Phys. Rev. C, replaced with corrected versio

Dynamics of Baryons from String Theory and Vector Dominance

We consider a holographic model of QCD from string theory, a la Sakai and Sugimoto, and study baryons. In this model, mesons are collectively realized as a five-dimensional \$U(N_F)=U(1)\times SU(N_F)$ Yang-Mills field and baryons are classically identified as $SU(N_F)$ solitons with a unit Pontryagin number and $N_c$ electric charges. The soliton is shown to be very small in the large 't Hooft coupling limit, allowing us to introduce an effective field ${\cal B}$. Its coupling to the mesons are dictated by the soliton structure, and consists of a direct magnetic coupling to the $SU(N_F)$ field strength as well as a minimal coupling to the $U(N_F)$ gauge field. Upon the dimensional reduction, this effective action reproduces all interaction terms between nucleons and an infinite tower of mesons in a manner consistent with the large $N_c$ expansion. We further find that all electromagnetic interactions, as inferred from the same effective action via a holographic prescription, are mediated by an infinite tower of vector mesons, rendering the baryon electromagnetic form factors completely vector-dominated as well. We estimate nucleon-meson couplings and also the anomalous magnetic moments, which compare well with nature.Comment: 65pages, 3 figures, vector mesons and axial-vector mesons are now canonically normalized (comparisons with data and conclusions unaffected

Absolute frequency measurement of the In+^{+} clock transition with a mode-locked laser

The absolute frequency of the In$^{+}$ $5s^{2 1}S_{0}$ - $5s5p^{3}P_{0}$ clock transition at 237 nm was measured with an accuracy of 1.8 parts in $10^{13}$. Using a phase-coherent frequency chain, we compared the $^{1}S_{0}$ - $^{3}P_{0}$ transition with a methane-stabilized He-Ne laser at 3.39 $\mu$m which was calibrated against an atomic cesium fountain clock. A frequency gap of 37 THz at the fourth harmonic of the He-Ne standard was bridged by a frequency comb generated by a mode-locked femtosecond laser. The frequency of the In$^{+}$ clock transition was found to be $1 267 402 452 899.92 (0.23)$ kHz, the accuracy being limited by the uncertainty of the He-Ne laser reference. This represents an improvement in accuracy of more than 2 orders of magnitude on previous measurements of the line and now stands as the most accurate measurement of an optical transition in a single ion.Comment: 3 pages, 2 figures. accepted for publication in Opt. Let