Van der Waals Density Functional for General Geometries

A scheme within density functional theory is proposed that provides a practical way to generalize to unrestricted geometries the method applied with some success to layered geometries [H. Rydberg, et al., Phys. Rev. Lett. 91, 126402 (2003)]. It includes van der Waals forces in a seamless fashion. By expansion to second order in a carefully chosen quantity contained in the long range part of the correlation functional, the nonlocal correlations are expressed in terms of a density-density interaction formula. It contains a relatively simple parametrized kernel, with parameters determined by the local density and its gradient. The proposed functional is applied to rare gas and benzene dimers, where it is shown to give a realistic description.Comment: 4 pages, 4 figure

Nature and strength of bonding in a crystal of semiconducting nanotubes: van der Waals density functional calculations and analytical results

The dispersive interaction between nanotubes is investigated through ab initio theory calculations and in an analytical approximation. A van der Waals density functional (vdW-DF) [Phys. Rev. Lett. 92, 246401 (2004)] is used to determine and compare the binding of a pair of nanotubes as well as in a nanotube crystal. To analyze the interaction and determine the importance of morphology, we furthermore compare results of our ab initio calculations with a simple analytical result that we obtain for a pair of well-separated nanotubes. In contrast to traditional density functional theory calculations, the vdW-DF study predicts an intertube vdW bonding with a strength that is consistent with recent observations for the interlayer binding in graphitics. It also produce a nanotube wall-to-wall separation which is in very good agreement with experiments. Moreover, we find that the vdW-DF result for the nanotube-crystal binding energy can be approximated by a sum of nanotube-pair interactions when these are calculated in vdW-DF. This observation suggests a framework for an efficient implementation of quantum-physical modeling of the CNT bundling in more general nanotube bundles, including nanotube yarn and rope structures.Comment: 10 pages, 4 figure

Enhanced dispersion interaction between quasi-one dimensional conducting collinear structures

Recent investigations have highlighted the failure of a sum of $R^{-6}$ terms to represent the dispersion interaction in parallel metallic, anisotropic, linear or planar nanostructures [J. F. Dobson, A. White, and A. Rubio, Phys. Rev. Lett. 96, 073201 (2006) and references therein]. By applying a simple coupled plasmon approach and using electron hydrodynamics, we numerically evaluate the dispersion (non-contact van der Waals) interaction between two conducting wires in a collinear pointing configuration. This case is compared to that of two insulating wires in an identical geometry, where the dispersion interaction is modelled both within a pairwise summation framework, and by adding a pinning potential to our theory leading to a standard oscillator-type model of insulating dielectric behavior. Our results provide a further example of enhanced dispersion interaction between two conducting nanosystems compared to the case of two insulating ones. Unlike our previous work, this calculation explores a region of relatively close coupling where, although the electronic clouds do not overlap, we are still far from the asymptotic region where a single power law describes the dispersion energy. We find that strong differences in dispersion attraction between metallic and semiconducting / insulating cases persist into this non-asymptotic region. While our theory will need to be supplemented with additional short-ranged terms when the electronic clouds overlap, it does not suffer from the short-distance divergence exhibited by purely asymptotic theories, and gives a natural saturation of the dispersion energy as the wires come into contact.Comment: 10 pages, 5 figures. Added new extended numerical calculations, new figures, extra references and heavily revised tex

FoldIndex©: a simple tool to predict whether a given protein sequence is intrinsically unfolded

Summary: An easy-to-use, versatile and freely available graphic web server, FoldIndex© is described: it predicts if a given protein sequence is intrinsically unfolded implementing the algorithm of Uversky and co-workers, which is based on the average residue hydrophobicity and net charge of the sequence. FoldIndex© has an error rate comparable to that of more sophisticated fold prediction methods. Sliding windows permit identification of large regions within a protein that possess folding propensities different from those of the whole protein. Availability: FoldIndex© can be accessed at http://bioportal.weizmann.ac.il/fldbin/findex Contact: [email protected] Supplementary information: http://www.weizmann.ac.il/sb/faculty_pages/Sussman/papers/suppl/Prilusky_200

Atomic Supersymmetry, Rydberg Wave Packets, and Radial Squeezed States

We study radial wave packets produced by short-pulsed laser fields acting on Rydberg atoms, using analytical tools from supersymmetry-based quantum-defect theory. We begin with a time-dependent perturbative calculation for alkali-metal atoms, incorporating the atomic-excitation process. This provides insight into the general wave packet behavior and demonstrates agreement with conventional theory. We then obtain an alternative analytical description of a radial wave packet as a member of a particular family of squeezed states, which we call radial squeezed states. By construction, these have close to minimum uncertainty in the radial coordinates during the first pass through the outer apsidal point. The properties of radial squeezed states are investigated, and they are shown to provide a description of certain aspects of Rydberg atoms excited by short-pulsed laser fields. We derive expressions for the time evolution and the autocorrelation of the radial squeezed states, and we study numerically and analytically their behavior in several alkali-metal atoms. Full and fractional revivals are observed. Comparisons show agreement with other theoretical results and with experiment.Comment: published in Physical Review

Semiconducting Monolayer Materials as a Tunable Platform for Excitonic Solar Cells

The recent advent of two-dimensional monolayer materials with tunable optoelectronic properties and high carrier mobility offers renewed opportunities for efficient, ultra-thin excitonic solar cells alternative to those based on conjugated polymer and small molecule donors. Using first-principles density functional theory and many-body calculations, we demonstrate that monolayers of hexagonal BN and graphene (CBN) combined with commonly used acceptors such as PCBM fullerene or semiconducting carbon nanotubes can provide excitonic solar cells with tunable absorber gap, donor-acceptor interface band alignment, and power conversion efficiency, as well as novel device architectures. For the case of CBN-PCBM devices, we predict the limit of power conversion efficiencies to be in the 10 - 20% range depending on the CBN monolayer structure. Our results demonstrate the possibility of using monolayer materials in tunable, efficient, polymer-free thin-film solar cells in which unexplored exciton and carrier transport regimes are at play.Comment: 7 pages, 5 figure

Unified Treatment of Asymptotic van der Waals Forces

In a framework for long-range density-functional theory we present a unified full-field treatment of the asymptotic van der Waals interaction for atoms, molecules, surfaces, and other objects. The only input needed consists of the electron densities of the interacting fragments and the static polarizability or the static image plane, which can be easily evaluated in a ground-state density-functional calculation for each fragment. Results for separated atoms, molecules, and for atoms/molecules outside surfaces are in agreement with those of other, more elaborate, calculations.Comment: 6 pages, 5 figure

Mechanical and Electronic Properties of MoS2_2 Nanoribbons and Their Defects

We present our study on atomic, electronic, magnetic and phonon properties of one dimensional honeycomb structure of molybdenum disulfide (MoS$_2$) using first-principles plane wave method. Calculated phonon frequencies of bare armchair nanoribbon reveal the fourth acoustic branch and indicate the stability. Force constant and in-plane stiffness calculated in the harmonic elastic deformation range signify that the MoS$_2$ nanoribbons are stiff quasi one dimensional structures, but not as strong as graphene and BN nanoribbons. Bare MoS$_2$ armchair nanoribbons are nonmagnetic, direct band gap semiconductors. Bare zigzag MoS$_2$ nanoribbons become half-metallic as a result of the (2x1) reconstruction of edge atoms and are semiconductor for minority spins, but metallic for the majority spins. Their magnetic moments and spin-polarizations at the Fermi level are reduced as a result of the passivation of edge atoms by hydrogen. The functionalization of MoS$_2$ nanoribbons by adatom adsorption and vacancy defect creation are also studied. The nonmagnetic armchair nanoribbons attain net magnetic moment depending on where the foreign atoms are adsorbed and what kind of vacancy defect is created. The magnetization of zigzag nanoribbons due to the edge states is suppressed in the presence of vacancy defects.Comment: 11 pages, 5 figures, first submitted at November 23th, 200

Many-body GW calculations of ground-state properties: Quasi-2D electron systems and van der Waals forces

We present GW many-body results for ground-state properties of two simple but very distinct families of inhomogeneous systems in which traditional implementations of density-functional theory (DFT) fail drastically. The GW approach gives notably better results than the well-known random-phase approximation, at a similar computational cost. These results establish GW as a superior alternative to standard DFT schemes without the expensive numerical effort required by quantum Monte Carlo simulations

FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded

An easy-to-use, versatile and freely available graphic web server, FoldIndex is described: it predicts if a given protein sequence is intrinsically unfolded implementing the algorithm of Uversky and co-workers, which is based on the average residue hydrophobicity and net charge of the sequence. FoldIndex has an error rate comparable to that of more sophisticated fold prediction methods. Sliding windows permit identification of large regions within a protein that possess folding propensities different from those of the whole protein