Simple models of the chemical field around swimming plankton

International audienceThe chemical field around swimming plankton depends on the swimming style and speed of the organism and the processes affecting uptake or exudation of chemicals by the organism. Here we present a simple model for the flow field around a neutrally buoyant self-propelled organism at low Reynolds number, and numerically calculate the chemical field around the organism. We show how the concentration field close to the organism and the mass transfer rates vary with swimming speed and style for Dirichlet (diffusion limited transport) boundary conditions. We calculate how the length of the chemical wake, defined as being the distance at which the chemical field drops to 10% of the surface concentration of the organism when stationary, varies with swimming speed and style for both Dirichlet and Neumann (production limited) boundary conditions. For Dirichlet boundary conditions, the length of the chemical wake increases with increasing swimming speed, and the self-propelled organism displays a significantly longer wake than the towed-body model. For the Neumann boundary conditions the converse is true; because swimming enhances the transport of the chemical away from the organism, the surface concentration of chemical is reduced and thus the wake length is reduced

Forces and conductances in a single-molecule bipyridine junction

Inspired by recent measurements of forces and conductances of bipyridine nano-junctions, we have performed density functional theory calculations of structure and electron transport in a bipyridine molecule attached between gold electrodes for seven different contact geometries. The calculations show that both the bonding force and the conductance are sensitive to the surface structure, and that both properties are in good agreement with experiment for contact geometries characterized by intermediate coordination of the metal atoms corresponding to a stepped surface. The conductance is mediated by the lowest unoccupied molecular orbital, which can be illustrated by a quantitative comparison with a one-level model. Implications for the interpretation of the experimentally determined force and conductance distributions are discussed

Image-charge induced localization of molecular orbitals at metal-molecule interfaces: Self-consistent GW calculations

Quasiparticle (QP) wave functions, also known as Dyson orbitals, extend the concept of single-particle states to interacting electron systems. Here we employ many-body perturbation theory in the GW approximation to calculate the QP wave functions for a semi-empirical model describing a $\pi$-conjugated molecular wire in contact with a metal surface. We find that image charge effects pull the frontier molecular orbitals toward the metal surface while orbitals with higher or lower energy are pushed away. This affects both the size of the energetic image charge shifts and the coupling of the individual orbitals to the metal substrate. Full diagonalization of the QP equation and, to some extent, self-consistency in the GW self-energy, is important to describe the effect which is not captured by standard density functional theory or Hartree-Fock. These results should be important for the understanding and theoretical modeling of electron transport across metal-molecule interfaces.Comment: 7 pages, 6 figure

Conduction Mechanism in a Molecular Hydrogen Contact

We present first principles calculations for the conductance of a hydrogen molecule bridging a pair of Pt electrodes. The transmission function has a wide plateau with T~1 which extends across the Fermi level and indicates the existence of a single, robust conductance channel with nearly perfect transmission. Through a detailed Wannier function analysis we show that the H2 bonding state is not involved in the transport and that the plateau forms due to strong hybridization between the H2 anti-bonding state and states on the adjacent Pt atoms. The Wannier functions furthermore allow us to derive a resonant-level model for the system with all parameters determined from the fully self-consistent Kohn-Sham Hamiltonian.Comment: 5 pages, 4 figure

Electron transport through an interacting region: The case of a nonorthogonal basis set

The formula derived by Meir and Wingreen [Phys. Rev. Lett. {\bf 68}, 2512 (1992)] for the electron current through a confined, central region containing interactions is generalized to the case of a nonorthogonal basis set. As in the original work, the present derivation is based on the nonequilibrium Keldysh formalism. By replacing the basis functions of the central region by the corresponding elements of the dual basis, the lead- and central region-subspaces become mutually orthogonal. The current formula is then derived in the new basis, using a generalized version of second quantization and Green's function theory to handle the nonorthogonality within each of the regions. Finally, the appropriate nonorthogonal form of the perturbation series for the Green's function is established for the case of electron-electron and electron-phonon interactions in the central region.Comment: Added references. 8 pages, 1 figur

The age of 47Tuc from self-consistent isochrone fits to colour-magnitude diagrams and the eclipsing member V69

Our aim is to derive a self-consistent age, distance and composition for the globular cluster $47\,$Tucanae ($47\,$Tuc; NGC104). First, we reevaluate the reddening towards the cluster resulting in a nominal $E(B-V)=0.03\pm0.01$ as the best estimate. The $T_{\rm eff}$ of the components of the eclipsing binary member V69 is found to be $5900\pm72$ K from both photometric and spectroscopic evidence. This yields a true distance modulus $(m-M)_0=13.21\pm0.06$(random)$\pm0.03$(systematic) to $47\,$Tuc when combined with existing measurements of V69 radii and luminosity ratio. We then present a new completely self-consistent isochrone fitting method to ground based and $\textit{HST}$ cluster colour-magnitude diagrams and the eclipsing binary member V69. The analysis suggests that the composition of V69, and by extension one of the populations of $47\,$Tuc, is given by [Fe/H]$\sim-0.70$, [O/Fe]$\sim+0.60$, and $Y\sim0.250$ on the solar abundance scale of Asplund, Grevesse & Sauval. However, this depends on the accuracy of the model $T_{\rm eff}$ scale which is 50-75 K cooler than our best estimate but within measurement uncertainties. Our best estimate of the age of $47\,$Tuc is 11.8 Gyr, with firm ($3 \sigma$) lower and upper limits of 10.4 and 13.4 Gyr, respectively, in satisfactory agreement with the age derived from the white dwarf cooling sequence if our determination of the distance modulus is adopted.Comment: 19 pages, 8 figures, accepted for publication in MNRA

Conserving GW scheme for nonequilibrium quantum transport in molecular contacts

We give a detailed presentation of our recent scheme to include correlation effects in molecular transport calculations using the GW approximation within the non-equilibrium Keldysh formalism. We restrict the GW self-energy to the central region, and describe the leads by density functional theory (DFT). A minimal basis of maximally localized Wannier functions is applied both in the central GW region and the leads. The importance of using a conserving, i.e. fully self-consistent, GW self-energy is demonstrated both analytically and by numerical examples. We introduce an effective spin-dependent interaction which automatically reduces self-interaction errors to all orders in the interaction. The scheme is applied to the Anderson model in- and out of equilibrium. In equilibrium at zero temperature we find that GW describes the Kondo resonance fairly well for intermediate interaction strengths. Out of equilibrium we demonstrate that the one-shot G0W0 approximation can produce severe errors, in particular at high bias. Finally, we consider a benzene molecule between featureless leads. It is found that the molecule's HOMO-LUMO gap as calculated in GW is significantly reduced as the coupling to the leads is increased, reflecting the more efficient screening in the strongly coupled junction. For the IV characteristics of the junction we find that HF and G0W0[G_HF] yield results closer to GW than does DFT and G0W0[G_DFT]. This is explained in terms of self-interaction effects and life-time reduction due to electron-electron interactions.Comment: 23 pages, 16 figure

Hybrid Local-Order Mechanism for Inversion Symmetry Breaking

Using classical Monte Carlo simulations, we study a simple statistical mechanical model of relevance to the emergence of polarisation from local displacements on the square and cubic lattices. Our model contains two key ingredients: a Kitaev-like orientation-dependent interaction between nearest neighbours, and a steric term that acts between next-nearest neighbours. Taken by themselves, each of these two ingredients is incapable of driving long-range symmetry breaking, despite the presence of a broad feature in the corresponding heat capacity functions. Instead each component results in a "hidden" transition on cooling to a manifold of degenerate states, the two manifolds are different in the sense that they reflect distinct types of local order. Remarkably, their intersection---\emph{i.e.} the ground state when both interaction terms are included in the Hamiltonian---supports a spontaneous polarisation. In this way, our study demonstrates how local ordering mechanisms might be combined to break global inversion symmetry in a manner conceptually similar to that operating in the "hybrid" improper ferroelectrics. We discuss the relevance of our analysis to the emergence of spontaneous polarisation in well-studied ferroelectrics such as BaTiO$_3$ and KNbO$_3$.Comment: 8 pages, 8 figure

Partly Occupied Wannier Functions

We introduce a scheme for constructing partly occupied, maximally localized Wannier functions (WFs) for both molecular and periodic systems. Compared to the traditional occupied WFs the partly occupied WFs posses improved symmetry and localization properties achieved through a bonding-antibonding closing procedure. We demonstrate the equivalence between bonding-antibonding closure and the minimization of the average spread of the WFs in the case of a benzene molecule and a linear chain of Pt atoms. The general applicability of the method is demonstrated through the calculation of WFs for a metallic system with an impurity: a Pt wire with a hydrogen molecular bridge.Comment: 5 pages, 4 figure

Strong plasmon-phonon splitting and hybridization in 2D materials revealed through a self-energy approach

We reveal new aspects of the interaction between plasmons and phonons in 2D materials that go beyond a mere shift and increase in plasmon width due to coupling to either intrinsic vibrational modes of the material or phonons in a supporting substrate. More precisely, we predict strong plasmon splitting due to this coupling, resulting in a characteristic avoided crossing scheme. We base our results on a computationally efficient approach consisting in including many-body interactions through the electron self-energy. We specify this formalism for a description of plasmons based upon a tight-binding electron Hamiltonian combined with the random-phase approximation. This approach is accurate provided vertex corrections can be neglected, as is is the case in conventional plasmon-supporting metals and Dirac-fermion systems. We illustrate our method by evaluating plasmonic spectra of doped graphene nanotriangles with varied size, where we predict remarkable peak splittings and other radical modifications in the spectra due to plasmons interactions with intrinsic optical phonons. Our method is equally applicable to other 2D materials and provides a simple approach for investigating coupling of plasmons to phonons, excitons, and other excitations in hybrid thin nanostructures