Controlled assembly of SNAP-PNA-fluorophore systems on DNA templates to produce fluorescence resonance energy transfer

The SNAP protein is a widely used self-labeling tag that can be used for tracking protein localization and trafficking in living systems. A model system providing controlled alignment of SNAP-tag units can provide a new way to study clustering of fusion proteins. In this work, fluorescent SNAP-PNA conjugates were controllably assembled on DNA frameworks forming dimers, trimers, and tetramers. Modification of peptide nucleic acid (PNA) with the O6-benzyl guanine (BG) group allowed the generation of site-selective covalent links between PNA and the SNAP protein. The modified BG-PNAs were labeled with fluorescent Atto dyes and subsequently chemo-selectively conjugated to SNAP protein. Efficient assembly into dimer and oligomer forms was verified via size exclusion chromatography (SEC), electrophoresis (SDS-PAGE), and fluorescence spectroscopy. DNA directed assembly of homo- and hetero-dimers of SNAP-PNA constructs induced homo- and hetero-FRET, respectively. Longer DNA scaffolds controllably aligned similar fluorescent SNAP-PNA constructs into higher oligomers exhibiting homo-FRET. The combined SEC and homo-FRET studies indicated the 1:1 and saturated assemblies of SNAP-PNA-fluorophore:DNA formed preferentially in this system. This suggested a kinetic/stoichiometric model of assembly rather than binomially distributed products. These BG-PNA-fluorophore building blocks allow facile introduction of fluorophores and/or assembly directing moieties onto any protein containing SNAP. Template directed assembly of PNA modified SNAP proteins may be used to investigate clustering behavior both with and without fluorescent labels which may find use in the study of assembly processes in cells

Shape Coexistence and the Effective Nucleon-Nucleon Interaction

The phenomenon of shape coexistence is discussed within the self-consistent Hartree-Fock method and the nuclear shell model. The occurrence of the coexisting configurations with different intrinsic shapes is traced back to the properties of the effective Hamiltonian.Comment: 40 pages (16 text, 24 figures). The file may also be retrieved at http://csep2.phy.ornl.gov/theory_group/people/dean/shape_coex/shapes.htm

Beta decay of r-process waiting-point nuclei in a self-consistent approach

Beta-decay rates for spherical neutron-rich r-process waiting-point nuclei are calculated within a fully self-consistent Quasiparticle Random-Phase Approximation, formulated in the Hartree-Fock-Bogolyubov canonical single-particle basis. The same Skyrme force is used everywhere in the calculation except in the proton-neutron particle-particle channel, where a finite-range force is consistently employed. In all but the heaviest nuclei, the resulting half-lives are usually shorter by factors of 2 to 5 than those of calculations that ignore the proton-neutron particle-particle interaction. The shorter half-lives alter predictions for the abundance distribution of r-process elements and for the time it takes to synthesize them.Comment: 14 pages RevTex, 10 eps figures, submitted to Phys. Rev.

Shell structure of superheavy nuclei in self-consistent mean-field models

We study the extrapolation of nuclear shell structure to the region of superheavy nuclei in self-consistent mean-field models -- the Skyrme-Hartree-Fock approach and the relativistic mean-field model -- using a large number of parameterizations. Results obtained with the Folded-Yukawa potential are shown for comparison. We focus on differences in the isospin dependence of the spin-orbit interaction and the effective mass between the models and their influence on single-particle spectra. While all relativistic models give a reasonable description of spin-orbit splittings, all non-relativistic models show a wrong trend with mass number. The spin-orbit splitting of heavy nuclei might be overestimated by 40%-80%. Spherical doubly-magic superheavy nuclei are found at (Z=114,N=184), (Z=120,N=172) or (Z=126,N=184) depending on the parameterization. The Z=114 proton shell closure, which is related to a large spin-orbit splitting of proton 2f states, is predicted only by forces which by far overestimate the proton spin-orbit splitting in Pb208. The Z=120 and N=172 shell closures predicted by the relativistic models and some Skyrme interactions are found to be related to a central depression of the nuclear density distribution. This effect cannot appear in macroscopic-microscopic models which have a limited freedom for the density distribution only. In summary, our findings give a strong argument for (Z=120,N=172) to be the next spherical doubly-magic superheavy nucleus.Comment: 22 pages REVTeX, 16 eps figures, accepted for publication in Phys. Rev.

Computer Microvision for Microelectromechanical Systems

Contains table of contents for Section 3 and reports on five research projects.Charles S. Draper Laboratory Contract DL-H-496015Defense Advanced Research Project Agency Grant F30602-97-2-0106W.M. Keck Foundation Career Development ProfessorshipAlfred P. Sloan Foundation Instrumentation Gran

Nuclear Skins and Halos in the Mean-Field Theory

Nuclei with large neutron-to-proton ratios have neutron skins, which manifest themselves in an excess of neutrons at distances greater than the radius of the proton distribution. In addition, some drip-line nuclei develop very extended halo structures. The neutron halo is a threshold effect; it appears when the valence neutrons occupy weakly bound orbits. In this study, nuclear skins and halos are analyzed within the self-consistent Skyrme-Hartree-Fock-Bogoliubov and relativistic Hartree-Bogoliubov theories for spherical shapes. It is demonstrated that skins, halos, and surface thickness can be analyzed in a model-independent way in terms of nucleonic density form factors. Such an analysis allows for defining a quantitative measure of the halo size. The systematic behavior of skins, halos, and surface thickness in even-even nuclei is discussed.Comment: 22 RevTeX pages, 22 EPS figures included, submitted to Physical Review

Shell Corrections of Superheavy Nuclei in Self-Consistent Calculations

Shell corrections to the nuclear binding energy as a measure of shell effects in superheavy nuclei are studied within the self-consistent Skyrme-Hartree-Fock and Relativistic Mean-Field theories. Due to the presence of low-lying proton continuum resulting in a free particle gas, special attention is paid to the treatment of single-particle level density. To cure the pathological behavior of shell correction around the particle threshold, the method based on the Green's function approach has been adopted. It is demonstrated that for the vast majority of Skyrme interactions commonly employed in nuclear structure calculations, the strongest shell stabilization appears for Z=124, and 126, and for N=184. On the other hand, in the relativistic approaches the strongest spherical shell effect appears systematically for Z=120 and N=172. This difference has probably its roots in the spin-orbit potential. We have also shown that, in contrast to shell corrections which are fairly independent on the force, macroscopic energies extracted from self-consistent calculations strongly depend on the actual force parametrisation used. That is, the A and Z dependence of mass surface when extrapolating to unknown superheavy nuclei is prone to significant theoretical uncertainties.Comment: 14 pages REVTeX, 8 eps figures, submitted to Phys. Rev.

Signal Transmission in the Auditory System

Contains table of contents for Section 3, an introduction and reports on five research projects.National Institutes of Health Grant R01-DC-00194National Institutes of Health Grant P01-DC-00119Charles S. Draper Laboratory Contract DL-H-496015National Institutes of Health Grant R01 DC00238National Institutes of Health Grant R01-DC02258National Institutes of Health Grant T32-DC00038National Institutes of Health Grant RO1 DC00235National Institutes of Health Grant P01-DC00361National Institutes of Health Contract N01-DC-6-210

Variable Stars in Galactic Globular Clusters

Based on a search of the literature up to May 2001, the number of known variable stars in Galactic globular clusters is approximately 3000. Of these, more than 2200 have known periods and the majority (approximately 1800) are of the RR Lyrae type. In addition to the RR Lyrae population, there are approximately 100 eclipsing binaries, 120 SX Phe variables, 60 Cepheids (including population II Cepheids, anomalous Cepheids and RV Tauri) and 120 SR/red variables. The mean period of the fundamental mode RR Lyrae variables is 0.585, for the overtone variables it is 0.342 (0.349 for the first-overtone pulsators and 0.296 for the second-overtone pulsators) and approximately 30% are overtone pulsators. These numbers indicate that about 65% of RR Lyrae variables in Galactic globular clusters belong to Oosterhoff type I systems. The mean period of the RR Lyrae variables in the Oosterhoff type I clusters seems to be correlated with metal abundance in the sense that the periods are longer in the more metal poor clusters. Such a correlation does not exist for the Oosterhoff type II clusters. Most of the Cepheids are in clusters with blue horizontal branches.Comment: 45 pages, 10 figures, to be published in AJ November 200

Signal Transmission in the Auditory System

Contains table of contents for Section 3, an introduction and reports on seven research projects.National Institutes of Health Grant P01-DC-00119National Institutes of Health Grant R01-DC-00194National Institutes of Health Grant R01 DC00238National Institutes of Health Grant R01-DC02258National Institutes of Health Grant T32-DC00038National Institutes of Health Grant P01-DC00361National Institutes of Health Grant 2RO1 DC00235National Institutes of Health Contract N01-DC2240