Theoretical description of protein field effects on electronic excitations of biological chromophores

Photoinitiated phenomena play a crucial role in many living organisms. Plants, algae, and bacteria absorb sunlight to perform photosynthesis, and convert water and carbon dioxide into molecular oxygen and carbohydrates, thus forming the basis for life on Earth. The vision of vertebrates is accomplished in the eye by a protein called rhodopsin, which upon photon absorption performs an ultrafast isomerisation of the retinal chromophore, triggering the signal cascade. Many other biological functions start with the photoexcitation of a protein-embedded pigment, followed by complex processes comprising, for example, electron or excitation energy transfer in photosynthetic complexes. The optical properties of chromophores in living systems are strongly dependent on the interaction with the surrounding environment (nearby protein residues, membrane, water), and the complexity of such interplay is, in most cases, at the origin of the functional diversity of the photoactive proteins. The specific interactions with the environment often lead to a significant shift of the chromophore excitation energies, compared with their absorption in solution or gas phase. The investigation of the optical response of chromophores is generally not straightforward, from both experimental and theoretical standpoints; this is due to the difficulty in understanding diverse behaviours and effects, occurring at different scales, with a single technique. In particular, the role played by ab initio calculations in assisting and guiding experiments, as well as in understanding the physics of photoactive proteins, is fundamental. At the same time, owing to the large size of the systems, more approximate strategies which take into account the environmental effects on the absorption spectra are also of paramount importance. Here we review the recent advances in the first-principle description of electronic and optical properties of biological chromophores embedded in a protein environment. We show their applications on paradigmatic systems, such as the light-harvesting complexes, rhodopsin and green fluorescent protein, emphasising the theoretical frameworks which are of common use in solid state physics, and emerging as promising tools for biomolecular systems

Ab-initio angle and energy resolved photoelectron spectroscopy with time-dependent density-functional theory

We present a time-dependent density-functional method able to describe the photoelectron spectrum of atoms and molecules when excited by laser pulses. This computationally feasible scheme is based on a geometrical partitioning that efficiently gives access to photoelectron spectroscopy in time-dependent density-functional calculations. By using a geometrical approach, we provide a simple description of momentum-resolved photoe- mission including multi-photon effects. The approach is validated by comparison with results in the literature and exact calculations. Furthermore, we present numerical photoelectron angular distributions for randomly oriented nitrogen molecules in a short near infrared intense laser pulse and helium-(I) angular spectra for aligned carbon monoxide and benzene.Comment: Accepted for publication on Phys. Rev.

Spin-Polarization transition in the two dimensional electron gas

We present a numerical study of magnetic phases of the 2D electron gas near freezing. The calculations are performed by diffusion Monte Carlo in the fixed node approximation. At variance with the 3D case we find no evidence for the stability of a partially polarized phase. With plane wave nodes in the trial function, the polarization transition takes place at Rs=20, whereas the best available estimates locate Wigner crystallization around Rs=35. Using an improved nodal structure, featuring optimized backflow correlations, we confirm the existence of a stability range for the polarized phase, although somewhat shrunk, at densities achievable nowadays in 2 dimensional hole gases in semiconductor heterostructures . The spin susceptibility of the unpolarized phase at the magnetic transition is approximately 30 times the Pauli susceptibility.Comment: 7 pages, 4 figure

Electronic and optical properties of doped TiO2 by many-body perturbation theory

Doping is one of the most common strategies for improving the photocatalytic and solar energy conversion properties of TiO2, hence an accurate theoretical description of the electronic and optical properties of doped TiO2 is of both scientific and practical interest. In this work we use many-body perturbation theory techniques to investigate two typical n-type dopants, niobium and hydrogen, in TiO2 rutile. Using the GW approximation to determine band edges and defect energy levels, and the Bethe-Salpeter equation for the calculation of the absorption spectra, we find that the defect energy levels form nondispersive bands lying 3c2.2 eV above the top of the corresponding valence bands ( 3c0.9 eV below the conduction bands of the pristine material). The defect states are also responsible for the appearance of low-energy absorption peaks that enhance the solar spectrum absorption of rutile. The spatial distributions of the excitonic wave functions associated with these low-energy excitations are very different for the two dopants, suggesting a larger mobility of photoexcited electrons in Nb-TiO2

Waterpipe smoking in students: Prevalence, risk factors, symptoms of addiction, and smoke intake. Evidence from one British university

Background: Anecdotal reports suggest waterpipe smoking is becoming common in students in western countries. The aim was to examine prevalence, risk factors, symptoms of addiction, and smoke intake. Methods: This was a cross-sectional survey of students with subsidiary survey of regular waterpipe user and survey of exhaled carbon monoxide (CO) before and after waterpipe smoking in customers of a waterpipe café. 937 students of Birmingham University completed the initial survey with a follow up of 21 regular waterpipe smokers. 63 customers of a waterpipe café near the University completed the study of CO intake. Results: 355 (37.9%, 95% confidence intervals (CI) 34.8 to 41.1%) students had tried waterpipes,the prevalence of trying rising with duration at University. 75 (8.0%, 95%CI 6.4 to 10.0%) were regular smokers, similar to the prevalence of cigarette smoking (9.4%). Although cigarette smoking was the major risk factor for being a regular waterpipe smoker, odds ratio (95%CI) 2.77 (1.52 to 5.06), 65% of waterpipe smokers did not smoke cigarettes. Seven of 21 (33.3%) regular waterpipe smokers experienced cravings. Nearly all regular waterpipe users thought it less harmful than smoking cigarettes. The mean (standard deviation) rise in CO was 37.4 (25.8)ppm, nearly twice as high as a typical cigarette smoker seeking cessation treatment. Conclusion: Waterpipe smoking is a common part of student culture in one British university, as in the Middle East and in the United States. It poses a potential threat to public health, with evidence of dependence and high smoke intake

Magnetic response and electronic states of well defined Graphene/Fe/Ir(111) heterostructure

We investigate a well defined heterostructure constituted by magnetic Fe layers sandwiched between graphene (Gr) and Ir(111). The challenging task to avoid Fe-C solubility and Fe-Ir intermixing has been achieved with atomic controlled Fe intercalation at moderate temperature below 500 K. Upon intercalation of a single ordered Fe layer in registry with the Ir substrate, an intermixing of the Gr bands and Fe d states breaks the symmetry of the Dirac cone, with a downshift in energy of the apex by about 3 eV, and well-localized Fe intermixed states induced in the energy region just below the Fermi level. First principles electronic structure calculations show a large spin splitting of the Fe states, resulting in a majority spin channel almost fully occupied and strongly hybridized with Gr π states. X-ray magnetic circular dichroism on the Gr/Fe/Ir heterostructure reveals an ordered spin configuration with a ferromagnetic response of Fe layer(s), with enhanced spin and orbital configurations with respect to the bcc-Fe bulk values. The magnetization switches from a perpendicular easy magnetization axis when the Fe single layer is lattice matched with the Ir(111) surface to a parallel one when the Fe thin film is almost commensurate with graphene

Empty electron states in cobalt-intercalated graphene

The dispersion of the electronic states of epitaxial graphene (Gr) depends significantly on the strength of the bonding with the underlying substrate. We report on empty electron states in cobalt-intercalated Gr grown on Ir(111), studied by angle-resolved inverse photoemission spectroscopy and x-ray absorption spectroscopy, complemented with density functional theory calculations. The weakly bonded Gr on Ir preserves the peculiar spectroscopic features of the Gr band structure, and the empty spectral densities are almost unperturbed. Upon intercalation of a Co layer, the electronic response of the interface changes, with an intermixing of the Gr π* bands and Co d states, which breaks the symmetry of π/σ states, and a downshift of the upper part of the Gr Dirac cone. Similarly, the image potential of Ir(111) is unaltered by the Gr layer, while a downward shift is induced upon Co intercalation, as unveiled by the image state energy dispersion mapped in a large region of the surface Brillouin zone

Correlation energy and spin polarization in the 2D electron gas

The ground state energy of the two--dimensional uniform electron gas has been calculated with fixed--node diffusion Monte Carlo, including backflow correlations, for a wide range of electron densities as a function of spin polarization. We give a simple analytic representation of the correlation energy which fits the density and polarization dependence of the simulation data and includes several known high- and low-density limits. This parametrization provides a reliable local spin density energy functional for two-dimensional systems and an estimate for the spin susceptibility. Within the proposed model for the correlation energy, a weakly first--order polarization transition occurs shortly before Wigner crystallization as the density is lowered.Comment: Minor typos corrected, see erratum: Phys. Rev. Lett. 91, 109902(E) (2003

Spin magnetization of strongly correlated electron gas confined in a two-dimensional finite lattice

The influence of disorder and interaction on the ground state polarization of the two-dimensional (2D) correlated electron gas is studied by numerical investigations of unrestricted Hartree-Fock equations. The ferromagnetic ground state is found to be plausible when the electron number is lowered and the interaction and disorder parameters are suitably chosen. For a finite system at constant electronic density the disorder induced spin polarization is cut off when the electron orbitals become strongly localized to the individual network sites. The fluctuations of the interaction matrix elements are calculated and brought out as favoring the ferromagnetic instability in the extended and weak localization regime. The localization effect of the Hubbard interaction term is discussed.Comment: 7 pages, 9 figure

The 2-D electron gas at arbitrary spin polarizations and arbitrary coupling strengths: Exchange-correlation energies, distribution functions and spin-polarized phases

We use a recent approach [Phys. Rev. Letters, {\bf 84}, 959 (2000)] for including Coulomb interactions in quantum systems via a classical mapping of the pair-distribution functions (PDFs) for a study of the 2-D electron gas. As in the 3-D case, the ``quantum temperature'' T_q of a classical 2-D Coulomb fluid which has the same correlation energy as the quantum fluid is determined as a function of the density parameter r_s. Spin-dependent exchange-correlation energies are reported. Comparisons of the spin-dependent pair-distributions and other calculated properties with any available 2-D quantum Monte Carlo (QMC) results show excellent agreement, strongly favouring more recent QMC data. The interesting novel physics brought to light by this study are: (a) the independently determined quantum-temperatures for 3-D and 2-D are found to be approximately the same, (i.e, universal) function of the classical coupling constant Gamma. (b) the coupling constant Gamma increases rapidly with r_s in 2-D, making it comparatively more coupled than in 3-D; the stronger coupling in 2-D requires bridge corrections to the hyper- netted-chain method which is adequate in 3-D; (c) the Helmholtz free energy of spin-polarized and unpolarized phases have been calculated. The existence of a spin-polarized 2-D liquid near r_s = 30, is found to be a marginal possibility. These results pertain to clean uniform 2-D electron systems.Comment: This paper replaces the cond-mat/0109228 submision; the new version include s more accurate numerical evaluation of the Helmholtz energies of the para- and ferromagentic 2D fluides at finite temperatures. (Paper accepted for publication in Phys. Rev. Lett.