First-principles energetics of water: a many-body analysis

Standard forms of density-functional theory (DFT) have good predictive power for many materials, but are not yet fully satisfactory for solid, liquid and cluster forms of water. We use a many-body separation of the total energy into its 1-body, 2-body (2B) and beyond-2-body (B2B) components to analyze the deficiencies of two popular DFT approximations. We show how machine-learning methods make this analysis possible for ice structures as well as for water clusters. We find that the crucial energy balance between compact and extended geometries can be distorted by 2B and B2B errors, and that both types of first-principles error are important.

First-principles energetics of water clusters and ice: a many-body analysis.

Standard forms of density-functional theory (DFT) have good predictive power for many materials, but are not yet fully satisfactory for cluster, solid, and liquid forms of water. Recent work has stressed the importance of DFT errors in describing dispersion, but we note that errors in other parts of the energy may also contribute. We obtain information about the nature of DFT errors by using a many-body separation of the total energy into its 1-body, 2-body, and beyond-2-body components to analyze the deficiencies of the popular PBE and BLYP approximations for the energetics of water clusters and ice structures. The errors of these approximations are computed by using accurate benchmark energies from the coupled-cluster technique of molecular quantum chemistry and from quantum Monte Carlo calculations. The systems studied are isomers of the water hexamer cluster, the crystal structures Ih, II, XV, and VIII of ice, and two clusters extracted from ice VIII. For the binding energies of these systems, we use the machine-learning technique of Gaussian Approximation Potentials to correct successively for 1-body and 2-body errors of the DFT approximations. We find that even after correction for these errors, substantial beyond-2-body errors remain. The characteristics of the 2-body and beyond-2-body errors of PBE are completely different from those of BLYP, but the errors of both approximations disfavor the close approach of non-hydrogen-bonded monomers. We note the possible relevance of our findings to the understanding of liquid water.

Reactive Many-Body Expansion for a Protonated Water Cluster.

We generalize the standard many-body expansion technique that is used to approximate the total energy of a molecular system to enable the treatment of chemical reactions by quantum chemical techniques. By considering all possible assignments of atoms to monomer units of the many-body expansion and associating suitable weights with each, we construct a potential energy surface that is a smooth function of the nuclear positions. We derive expressions for this reactive many-body expansion energy and describe an algorithm for its evaluation, which scales polynomially with system size, and therefore will make the method feasible for future condensed phase simulations. We demonstrate the accuracy and smoothness of the resulting potential energy surface on a molecular dynamics trajectory of the protonated water hexamer, using the Hartree-Fock method for the many-body term and Møller-Plesset theory for the low order terms of the many-body expansion.

Single-particle probing of edge-state formation in a graphene nanoribbon

We investigate the effect of a perpendicular magnetic field on the single-particle charging spectrum of a graphene quantum dot embedded inline with a nanoribbon. We observe uniform shifts in the single-particle spectrum which coincide with peaks in the magnetoconductance, implicating Landau level condensation and edge state formation as the mechanism underlying magnetic field-enhanced transmission through graphene nanostructures. The experimentally determined ratio of bulk to edge states is supported by single-particle band-structure simulations, while a fourfold beating of the Coulomb blockade transmission amplitude points to many-body interaction effects during Landau level condensation of the ν=0 state. © 2012 American Physical Society.

Accurate screened exchange band structures for the transition metal monoxides MnO, FeO, CoO and NiO.

We report calculations of the band structures and density of states of the four transition metal monoxides MnO, FeO, CoO and NiO using the hybrid density functional sX-LDA ('screened exchange local density approximation'). Late transition metal oxides are prototypical examples of strongly correlated materials, which pose challenges for electronic structure methods. We compare our results with available experimental data and show that our calculations generally yield accurate predictions for the fundamental band gaps and valence bands, in favourable agreement with previously reported theoretical studies. For MnO, the band gaps are still underestimated, suggesting additional many-body effects that are not captured by our screened hybrid functional approach.

Ultrafast collinear scattering and carrier multiplication in graphene.

Graphene is emerging as a viable alternative to conventional optoelectronic, plasmonic and nanophotonic materials. The interaction of light with charge carriers creates an out-of-equilibrium distribution, which relaxes on an ultrafast timescale to a hot Fermi-Dirac distribution, that subsequently cools emitting phonons. Although the slower relaxation mechanisms have been extensively investigated, the initial stages still pose a challenge. Experimentally, they defy the resolution of most pump-probe setups, due to the extremely fast sub-100 fs carrier dynamics. Theoretically, massless Dirac fermions represent a novel many-body problem, fundamentally different from Schrödinger fermions. Here we combine pump-probe spectroscopy with a microscopic theory to investigate electron-electron interactions during the early stages of relaxation. We identify the mechanisms controlling the ultrafast dynamics, in particular the role of collinear scattering. This gives rise to Auger processes, including charge multiplication, which is key in photovoltage generation and photodetectors.

Nearly intrinsic exciton lifetimes in single twin-free GaAsAlGaAs core-shell nanowire heterostructures

CW and time-resolved photoluminescence measurements are used to investigate exciton recombination dynamics in GaAsAlGaAs heterostructure nanowires grown with a recently developed technique which minimizes twinning. A thin capping layer is deposited to eliminate the possibility of oxidation of the AlGaAs shell as a source of oxygen defects in the GaAs core. We observe exciton lifetimes of ∼1 ns, comparable to high quality two-dimensional double heterostructures. These GaAs nanowires allow one to observe state filling and many-body effects resulting from the increased carrier densities accessible with pulsed laser excitation. © 2008 American Institute of Physics.

Fano resonance in Raman scattering of graphene

Fano resonances and their strong doping dependence are observed in Raman scattering of single-layer graphene (SLG). As the Fermi level is varied by a back-gate bias, the Raman G band of SLG exhibits an asymmetric line shape near the charge neutrality point as a manifestation of a Fano resonance, whereas the line shape is symmetric when the graphene sample is electron or hole doped. However, the G band of bilayer graphene (BLG) does not exhibit any Fano resonance regardless of doping. The observed Fano resonance can be interpreted as interferences between the phonon and excitonic many-body spectra in SLG. The absence of a Fano resonance in the Raman G band of BLG can be explained in the same framework since excitonic interactions are not expected in BLG. © 2013 Elsevier Ltd. All rights reserved.

Spread of Salmonella enterica in the body during systemic infection: unravelling host and pathogen determinants.

Salmonella enterica causes a range of life-threatening diseases in humans and animals worldwide. Current treatments for S. enterica infections are not sufficiently effective, and there is a need to develop new vaccines and therapeutics. An understanding of how S. enterica spreads in tissues has very important implications for targeting bacteria with vaccine-induced immune responses and antimicrobial drugs. Development of new control strategies would benefit from a more sophisticated evaluation of bacterial location, spatiotemporal patterns of spread and distribution in the tissues, and sites of microbial persistence. We review here recent studies of S. enterica serovar Typhimurium (S. Typhimurium) infections in mice, an established model of systemic typhoid fever in humans, which suggest that continuous bacterial spread to new infection foci and host phagocytes is an essential trait in the virulence of S. enterica during systemic infections. We further highlight how infections within host tissues are truly heterogeneous processes despite the fact that they are caused by the expansion of a genetically homogeneous microbial population. We conclude by discussing how understanding the within-host quantitative, spatial and temporal dynamics of S. enterica infections might aid the development of novel targeted preventative measures and drug regimens.