Secondary-Structure Design of Proteins by a Backbone Torsion Energy

We propose a new backbone-torsion-energy term in the force field for protein systems. This torsion-energy term is represented by a double Fourier series in two variables, the backbone dihedral angles phi and psi. It gives a natural representation of the torsion energy in the Ramachandran space in the sense that any two-dimensional energy surface periodic in both phi and psi can be expanded by the double Fourier series. We can then easily control secondary-structure-forming tendencies by modifying the torsion-energy surface. For instance, we can increase/decrease the alpha-helix-forming-tendencies by lowering/raising the torsion-energy surface in the alpha-helix region and likewise increase/decrease the beta-sheet-forming tendencies by lowering/raising the surface in the beta-sheet region in the Ramachandran space. We applied our approach to AMBER parm94 and AMBER parm96 force fields and demonstrated that our modifications of the torsion-energy terms resulted in the expected changes of secondary-structure-forming-tendencies by performing folding simulations of alpha-helical and beta-hairpin peptides.Comment: 13 pages, (Revtex4), 5 figure

Electronic and Magnetic Phase Diagram of a Superconductor, SmFeAsO1-xFx

A crystallographic and magnetic phase diagram of SmFeAsO1-xFx is determined as a function of x in terms of temperature based on electrical transport and magnetization, synchrotron powder x-ray diffraction, 57Fe Mossbauer spectra (MS), and 149Sm nuclear resonant forward scattering (NRFS) measurements. MS revealed that the magnetic moments of Fe were aligned antiferromagnetically at ~144 K (TN(Fe)). The magnetic moment of Fe (MFe) is estimated to be 0.34 myuB/Fe at 4.2 K for undoped SmFeAsO; MFe is quenched in superconducting F-doped SmFeAsO. 149Sm NRFS spectra revealed that the magnetic moments of Sm start to order antiferromagnetically at 5.6 K (undoped) and 4.4 K (TN(Sm)) (x = 0.069). Results clearly indicate that the antiferromagnetic Sm sublattice coexists with the superconducting phase in SmFeAsO1-xFx below TN(Sm), while antiferromagnetic Fe sublattice does not coexist with the superconducting phase.Comment: Accepted in New Journal of Physic

AN EXPERIMENTAL AND MODELING STUDY OF ELECTROOSMOTIC BULK AND NEAR-WALL FLOWS IN TWO-DIMENSIONAL MICRO-AND NANOCHANNELS

ABSTRACT Electrokinetically driven flow of electrolyte solutions through micro-and nanochannels is of interest in microelectromechanical systems (MEMS) and nanotechnology applications. In this work, fully developed and steady electroosmotic flow (EOF) of dilute sodium tetraborate and sodium chloride aqueous solutions in a rectangular channel where the channel height h is comparable to its width W is examined. EOF is also studied under conditions of electric double layer (EDL) overlap, or λ/h ~ O(1), where λ is the Debye thickness, for very dilute solutions. The initial experimental data and model results are in very good agreement for dilute sodium tetraborate solutions. The experimental work uses the new nano-particle image velocimetry (nPIV) technique. Evanescent waves from the total internal reflection of light with a wavelength of 488 nm at a refractive index interface is used to illuminate 100 nm neutrally buoyant fluorescent particles in the near-wall region of the flow. The images of these tracer particles over time are processed to obtain the two components of the velocity field parallel to the wall in fully developed EOF of sodium tetraborate at concentrations up to 2 mM in fused quartz rectangular channels with height h up to 10 microns. The spatial resolution of these velocity field data along the dimension normal to the wall is about 100 nm, and the data are obtained within a distance of approximately 100 nm of the wall based upon the 1/e intensity point, or penetration depth. A set of equations modeling EOF in a long channel are solved where h/L << 1, and L is the lengthscale along the flow direction. Unlike most previous models, this work does not use the Debye-Huckel approximation, nor does it assume symmetric boundary conditions. For the case where λ/h << 1, analytical solutions for the velocity, potential and mole fractions are obtained using an asymptotic perturbation approach

Interaction induced collapse of a section of the Fermi sea in in the zig-zag Hubbard ladder

Using the next-nearest neighbor (zig-zag) Hubbard chain as an one dimemensional model, we investigate the influence of interactions on the position of the Fermi wavevectors with the density-matrix renormalization-group technique (DMRG). For suitable choices of the hopping parameters we observe that electron-electron correlations induce very different renormalizations for the two different Fermi wavevectors, which ultimately lead to a complete destruction of one section of the Fermi sea in a quantum critical point

Perturbation expansion for 2-D Hubbard model

We develop an efficient method to calculate the third-order corrections to the self-energy of the hole-doped two-dimensional Hubbard model in space-time representation. Using the Dyson equation we evaluate the renormalized spectral function in various parts of the Brillouin zone and find significant modifications with respect to the second-order theory even for rather small values of the coupling constant U. The spectral function becomes unphysical for $U \simeq W$, where W is the half-width of the conduction band. Close to the Fermi surface and for U<W, the single-particle spectral weight is reduced in a finite energy interval around the Fermi energy. The increase of U opens a gap between the occupied and unoccupied parts of the spectral function.Comment: 17 pages, 11 Postscript figures, Phys. Rev. B, accepte

Social Interactions of Juvenile Brown Boobies at Sea as Observed with Animal-Borne Video Cameras

While social interactions play a crucial role on the development of young individuals, those of highly mobile juvenile birds in inaccessible environments are difficult to observe. In this study, we deployed miniaturised video recorders on juvenile brown boobies Sula leucogaster, which had been hand-fed beginning a few days after hatching, to examine how social interactions between tagged juveniles and other birds affected their flight and foraging behaviour. Juveniles flew longer with congeners, especially with adult birds, than solitarily. In addition, approximately 40% of foraging occurred close to aggregations of congeners and other species. Young seabirds voluntarily followed other birds, which may directly enhance their foraging success and improve foraging and flying skills during their developmental stage, or both