Electronic structure of multiquantum giant vortex states in mesoscopic superconducting disks

We report self-consistent calculations of the microscopic electronic structure of the so-called giant vortex states. These novel multiquantum vortex states, detected by recent magnetization measurements on submicron disks, are qualitatively different from the Abrikosov vortices in the bulk. We find that, in addition to multiple branches of bound states in the core region, the local tunneling density of states exhibits Tomasch oscillations due to the single-particle interference arising from quantum confinement. These features should be directly observable by scanning tunneling spectroscopy.Comment: 5 pages, 4 figure

Quasiparticle States at a d-Wave Vortex Core in High-Tc Superconductors: Induction of Local Spin Density Wave Order

The local density of states (LDOS) at one of the vortex lattice cores in a high Tc superconductor is studied by using a self-consistent mean field theory including interactions for both antiferromagnetism (AF) and d-wave superconductivity (DSC). The parameters are chosen in such a way that in an optimally doped sample the AF order is completely suppressed while DSC prevails. In the mixed state, we show that the local AF-like SDW order appears near the vortex core and acts as an effective local magnetic field on the quasiparticles. As a result, the LDOS at the core exhibits a double-peak structure near the Fermi level that is in good agreement with the STM observations on YBCO and BSCCO. The presence of local AF order near the votex core is also consistent with the recent neutron scattering experiment on LSCO.Comment: 4 pages, 2 ps figure

A Self-Consistent Microscopic Theory of Surface Superconductivity

The electronic structure of the superconducting surface sheath in a type-II superconductor in magnetic fields $H_{c2}<H<H_{c3}$ is calculated self-consistently using the Bogoliubov-de Gennes equations. We find that the pair potential $\Delta(x)$ exhibits pronounced Friedel oscillations near the surface, in marked contrast with the results of Ginzburg-Landau theory. The role of magnetic edge states is emphasized. The local density of states near the surface shows a significant depletion near the Fermi energy due to the development of local superconducting order. We suggest that this structure could be unveiled by scanning-tunneling microscopy studies performed near the edge of a superconducting sample.Comment: 12 pages, Revtex 3.0, 3 postscript figures appende

Ab initio Molecular Dynamics in Adaptive Coordinates

We present a new formulation of ab initio molecular dynamics which exploits the efficiency of plane waves in adaptive curvilinear coordinates, and thus provides an accurate treatment of first-row elements. The method is used to perform a molecular dynamics simulation of the CO_2 molecule, and allows to reproduce detailed features of its vibrational spectrum such as the splitting of the Raman sigma+_g mode caused by Fermi resonance. This new approach opens the way to highly accurate ab initio simulations of organic compounds.Comment: 11 pages, 3 PostScript figure

Local density of states in the vortex lattice in a type II superconductor

Local density of states (LDOS) in the triangular vortex lattice is investigated based on the quasi-classical Eilenberger theory. We consider the case of an isotropic s-wave superconductor with the material parameter appropriate to NbSe_2. At a weak magnetic field, the spatial variation of the LDOS shows cylindrical structure around a vortex core. On the other hand, at a high field where the core regions substantially overlap each other, the LDOS is sixfold star-shaped structure due to the vortex lattice effect. The orientation of the star coincides with the experimental data of the scanning tunneling microscopy. That is, the ray of the star extends toward the nearest-neighbor (next nearest-neighbor) vortex direction at higher (lower) energy.Comment: 10 pages, RevTex, 32 figure

Real-space local polynomial basis for solid-state electronic-structure calculations: A finite-element approach

We present an approach to solid-state electronic-structure calculations based on the finite-element method. In this method, the basis functions are strictly local, piecewise polynomials. Because the basis is composed of polynomials, the method is completely general and its convergence can be controlled systematically. Because the basis functions are strictly local in real space, the method allows for variable resolution in real space; produces sparse, structured matrices, enabling the effective use of iterative solution methods; and is well suited to parallel implementation. The method thus combines the significant advantages of both real-space-grid and basis-oriented approaches and so promises to be particularly well suited for large, accurate ab initio calculations. We develop the theory of our approach in detail, discuss advantages and disadvantages, and report initial results, including the first fully three-dimensional electronic band structures calculated by the method.Comment: replacement: single spaced, included figures, added journal referenc

Model peptides to study the effects of P2 and P3 substitutions in statine-containing HIV proteinase inhibitors

AbstractThrough a series of synthetic model peptides, we have examined the structural requirements of the P2 and P3 residues in statine-based HIV protease (PR) inhibitors. Results agree with the general observations that, the more bulky the P3 aromatic hydrophobic side chain, the more potent is the inhibitor. At P2, an isopropyl side chain is critical in maintaining potency. Three-dimensional modeling demonstrates that the steric bulk of a leucyl residue or the unfavorable energy transfer, from water to enzyme, for a basic amino acid residue at P2 markedly compromises activity. A naphthylalaninyl-valyl P3-P2 substituted analogue inhibits PR with an IC50 value of 6 nM, and was also effective as an antiviral agent

Large-scale proteomic analysis of T. spiralis muscle-stage ESPs identifies a novel upstream motif for in silico prediction of secreted products

The Trichinella genus contains parasitic nematodes capable of infecting a wide range of hosts including mammals, birds and reptiles. Like other helminths, T. spiralis secretes a complex mixture of bioactive molecules capable of modulating its immediate surroundings and creating a hospitable environment for growth, survival and ultimately transmission. The constitution of these excretory-secretory products (ESPs) changes depending on the tissue niche and the specific stage of parasite development. Unique to T. spiralis is a true intracellular stage wherein larvae develop inside striated myotubes. Remarkably, the parasite larvae do not destroy the host cell but rather reprogram it to support their presence and growth. This transformation is largely mediated through stage-specific secretions released into the host cell cytoplasm. In this study, we apply state of the art proteomics and computational approaches to elucidate the composition and functions of muscle-stage T. spiralis ESPs. Moreover, we define a recurring, upstream motif associated with the stichosome, the main secretory organ of this worm, and can be used to predict secreted proteins across experimentally less tractable T. spiralis life cycle stages

Dirac quasiparticles in the mixed state

Energies and wave functions are calculated for d-wave quasiparticles in the mixed state using the formalism of Franz and Tesanovic for the low-lying energy levels. The accuracy of the plane-wave expansion is explored by comparing approximate to exact results for a simplified one-dimensional problem, and the convergence of the plane- wave expansion to the two-dimensional case is studied. The results are used to calculate the low-energy tunneling density of states and the low-temperature specific heat, and these theoretical results are compared to semiclassical treatments and to the available data. Implications for the muon spin resonance measurements of vortex core size are also discussed.Comment: 13 pages, 15 figures, RevTeX. References corrected. A factor of 2 in the results has been corrected, and the conclusions have been update

Understanding the Mechanism of Human P450 CYP1A2 Using Coupled Quantum-Classical Simulations in a Dynamical Environment

The reaction mechanism of the human P450 CYP1A2 enzyme plays a fundamental role in understanding the effects of environmental carcinogens and mutagens on humans. Despite extensive experimental research on this enzyme system, key questions regarding its catalytic cycle and oxygen activation mechanism remain unanswered. In order to elucidate the reaction mechanism in human P450, new computational methods are needed to accurately represent this system. To enable us to perform computational simulations of unprecedented accuracy on these systems, we developed a dynamic quantum-classical (QM/MM) hybrid method, in which ab initio molecular dynamics are coupled with classical molecular mechanics. This will provide the accuracy needed to address such a complex, large biological system in a fully dynamic environment. We also present detailed calculations of the P450 active site, including the relative charge transfer between iron porphine and tetraphenyl porphyrin