Effect of stoichiometry on the magnetocrystalline anisotropy of Fe-Pt and Co-Pt from first-principles calculation.

The effect of stoichiometry on magnetocrystalline anisotropy energy (MAE) of Fe1+xPt1-x and Co1+xPt1-x (-0.5 < x < 0.5) is studied by use of first-principles method. The calculated MAEs show maxima at x = 0 for both fully L10-ordered systems. Compared with that, the MAEs of partially L10-ordered systems reduce but their composition dependences do not change, without shift of the maximum MAE to Fe/Co-rich alloy as found in experiment at room temperature. In the off-stoichiometric alloys, the misoccupied Fe/Co and Pt show large MAEs, which is explained by the enhanced in-plane hybridization between Fe/Co and Pt. The composition dependence of the atom-resolved MAE is governed by the varying number of heterogeneous ligands around the atom. The MAE(T)/MAE(0) is discussed based on spontaneous magnetization and Curie temperature, which suggests that the temperature effect may contribute to the discrepancy between calculation and experiment in the composition dependence of MAE.

Light-harvesting processes in the dynamic photosynthetic antenna.

We present our perspective on the theoretical basis of light-harvesting within the photosynthetic membrane. Far from being a static structure, the photosynthetic membrane is a highly dynamic system, with protein mobility playing an important role in the damage/repair cycle of photosystem II (PSII), in balancing the input of energy between PSI and PSII, and in the photoprotection of PSII in response to a sudden excess of illumination. The concept of a photosynthetic antenna is illustrated and the state transition phenomenon is discussed as an example of purposeful antenna mobility. We discuss fluorescence recovery after photo-bleaching as a technique for visualising membrane mobility, before introducing light-induced grana membrane reorganisation as an integral part of the rapid photoprotective switch in plants. We then discuss current theoretical approaches to modelling the energy transfer dynamics of the PSII antenna: the atomistic models of intra-complex transfer and the coarse-grained approach to the inter-complex dynamics. Finally we discuss the future prospect of extending these methods, beyond the static picture of the membrane, to the dynamic PSII photosynthetic antenna.

Quantum mechanical calculations of xanthophyll-chlorophyll electronic coupling in the light-harvesting antenna of photosystem II of higher plants.

Light-harvesting by the xanthophylls in the antenna of photosystem II (PSII) is a very efficient process (with 80% of the absorbed energy being transfer to chlorophyll). However, the efficiencies of the individual xanthophylls vary considerably, with violaxanthin in LHCII contributing very little to light-harvesting. To investigate the origin of the variation we used Time Dependent Density Functional Theory to model the Coulombic interactions between the xanthophyll 1(1)B(u)(+) states and the chlorophyll Soret band states in the LHCII and CP29 antenna complexes. The results show that the central L1 and L2 binding sites in both complexes favored close cofacial associations between the bound xanthophylls and chlorophyll a, implying efficient energy transfer, consistent with previously reported experimental evidence. Additionally, we found that the peripheral V1 binding site in LHCII did not favor close xanthophyll-chlorophyll associations, confirming observations that violaxanthin in LHCII is not an effective light-harvester. Finally, violaxanthin bound into the L2 site of the CP29 complex was found to be very strongly coupled to its neighboring chlorophylls.

Modeling of fluorescence quenching by lutein in the plant light-harvesting complex LHCII.

Photoprotective non-photochemical quenching (NPQ) in higher plants is the result of the formation of energy quenching traps in the light-harvesting antenna of photosystem II (PSII). It has been proposed that this quenching trap is a lutein molecule closely associated with the chlorophyll terminal emitter of the major light-harvesting complex LHCII. We have used a combination of time-dependent density functional theory (TD-DFT) and the semiempirical MNDO-CAS-CI method to model the chlorophyll-lutein energy transfer dynamics of the highly quenched crystal structure of LHCII. Our calculations reveal that the incoherent "hopping" of energy from Chla612 to the short-lived, dipole forbidden 2(1)A(g)(-) state of lutein620 accounts for the strong fluorescence quenching observed in these crystals. This adds weight to the argument that the same dissipative pathway is responsible for in vivo NPQ.

Importance of correlation effects in hcp iron revealed by a pressure-induced electronic topological transition.

We discover that hcp phases of Fe and Fe(0.9)Ni(0.1) undergo an electronic topological transition at pressures of about 40 GPa. This topological change of the Fermi surface manifests itself through anomalous behavior of the Debye sound velocity, c/a lattice parameter ratio, and Mössbauer center shift observed in our experiments. First-principles simulations within the dynamic mean field approach demonstrate that the transition is induced by many-electron effects. It is absent in one-electron calculations and represents a clear signature of correlation effects in hcp Fe.

Effect of temperature on the elastic anisotropy of pure Fe and Fe0.9Cr0.1 random alloy.

The elastic properties of pure iron and substitutionally disordered 10 at. % Cr Fe-Cr alloy are investigated as a function of temperature by using first-principles electronic-structure calculations by the exact muffin-tin orbitals method. The temperature effects on the elastic properties are included via the electronic, magnetic, and lattice expansion contributions. We show that the degree of magnetic order in both pure iron and Fe(90)Cr(10) alloy mainly determines the dramatic change of the elastic anisotropy of these materials at elevated temperatures. The effect of lattice expansion is found to be secondary but also very important for quantitative modeling.

A theoretical investigation of the photophysical consequences of major plant light-harvesting complex aggregation within the photosynthetic membrane.

Spectroscopic measurements of Arabidopsis leaves have shown that the energy-dependent component of non-photochemical quenching (NPQ), known as qE, is associated with an absorption change at 535 nm (ΔA(535)). Identical measurements on the zeaxanthin-deficient mutant npq1 reveal a similar spectroscopic signature at 525 nm (ΔA(525)). We investigated whether these red-shifts may arise from excitonic interactions among homodimers of xanthophylls, zeaxanthin, and violaxanthin, bound at the peripheral V1 binding site on adjacent light-harvesting complex II (LHCII) trimers. Estimates of the relative geometries of these pigment pairs were obtained from the structure of LHCII. The excitonic couplings of zeaxanthin and violaxanthin dimers were probed using the time-dependent density functional theory method (TD-DFT). Calculations indicated that dimers formed between zeaxanthin or violaxanthin molecules using the published LHCII structure resulted in absorption blue shifts, typical of an H-type (parallel) geometry. In contrast, if the volume of the LHCII structure was modified to reflect the change in membrane thickness that occurs upon ΔpH formation, then both zeaxanthin and violaxanthin dimers adopted a J-type (collinear) geometry, and the resulting spectral shift was to the red region. The magnitudes of these predicted red-shifts are in good agreement with the experimental magnitudes. We therefore conclude that the observed xanthophyll red-shift results from the combination of both LHCII aggregation and changes in membrane thickness during qE. ΔA(535) may therefore be considered a "marker of aggregation" between LHCII trimers upon qE formation.

Influence of the magnetic state on the chemical order-disorder transition temperature in Fe-Ni permalloy.

In magnetic alloys, the effect of finite temperature magnetic excitations on phase stability below the Curie temperature is poorly investigated, although many systems undergo phase transitions in this temperature range. We consider random Ni-rich Fe-Ni alloys, which undergo chemical order-disorder transition approximately 100 K below their Curie temperature, to demonstrate from ab initio calculations that deviations of the global magnetic state from ideal ferromagnetic order due to temperature induced magnetization reduction have a crucial effect on the chemical transition temperature. We propose a scheme where the magnetic state is described by partially disordered local magnetic moments, which in combination with Heisenberg Monte Carlo simulations of the magnetization allows us to reproduce the transition temperature in good agreement with experimental data.

Stability in bcc transition metals: Madelung and band-energy effects due to alloying.

The phase stability of group VB (V, Nb, and Ta) transition metals is explored by first-principles electronic-structure calculations. Alloying with a small amount of a neighboring metal can either stabilize or destabilize the body-centered-cubic phase relative to low-symmetry rhombohedral phases. We show that band-structure effects determine phase stability when a particular group VB metal is alloyed with its nearest neighbors within the same d-transition series. In this case, the neighbor with less (to the left) and more (to the right) d electrons destabilize and stabilize bcc, respectively. When alloying with neighbors of higher d-transition series, electrostatic Madelung energy dominates and stabilizes the body-centered-cubic phase. This surprising prediction invalidates current understanding of simple d-electron bonding that dictates high-symmetry cubic and hexagonal phases.

Antisite-defect-induced surface segregation in ordered NiPt alloy.

By means of first principles simulations we demonstrate that tiny deviations from stoichiometry in the bulk composition of the NiPt-L1(0) ordered alloy have a great impact on the atomic configuration of the (111) surface. We predict that at T=600 K the (111) surface of the Ni51Pt49 and Ni50Pt50 alloys corresponds to the (111) truncation of the bulk L1(0) ordered structure. However, the (111) surface of the nickel deficient Ni49Pt51 alloy is strongly enriched by Pt and should exhibit the pattern of the 2x2 structure. Such a drastic change in the segregation behavior is due to the presence of different antisite defects in the Ni- and Pt-rich alloys and is a manifestation of the so-called off-stoichiometric effect.

Plants lacking the main light-harvesting complex retain photosystem II macro-organization.

Photosystem II (PSII) is a key component of photosynthesis, the process of converting sunlight into the chemical energy of life. In plant cells, it forms a unique oligomeric macrostructure in membranes of the chloroplasts. Several light-harvesting antenna complexes are organized precisely in the PSII macrostructure-the major trimeric complexes (LHCII) that bind 70% of PSII chlorophyll and three minor monomeric complexes-which together form PSII supercomplexes. The antenna complexes are essential for collecting sunlight and regulating photosynthesis, but the relationship between these functions and their molecular architecture is unresolved. Here we report that antisense Arabidopsis plants lacking the proteins that form LHCII trimers have PSII supercomplexes with almost identical abundance and structure to those found in wild-type plants. The place of LHCII is taken by a normally minor and monomeric complex, CP26, which is synthesized in large amounts and organized into trimers. Trimerization is clearly not a specific attribute of LHCII. Our results highlight the importance of the PSII macrostructure: in the absence of one of its main components, another protein is recruited to allow it to assemble and function.

Combined electronic structure and evolutionary search approach to materials design.

We show that density functional theory calculations have reached an accuracy and speed making it possible to use them in conjunction with an evolutionary algorithm to search for materials with specific properties. The approach is illustrated by finding the most stable four component alloys out of the 192 016 possible fcc and bcc alloys that can be constructed out of 32 different metals. A number of well known and new "super alloys" are identified in this way.

Ab initio study of phase equilibria in TiC(x).

The phase diagram for the vacancy-ordered structures in the substoichiometric TiC(x) (x = 0.5-1.0) has been established from Monte Carlo simulations with the long-range pair and multisite effective interactions obtained from ab initio calculations. Three ordered superstructures of vacancies (Ti(2)C, Ti(3)C(2), and Ti(6)C(5)) are found to be ground state configurations. Their stability has been verified by full-potential total energy calculations of the fully relaxed structures.

Kinetic analysis of nonphotochemical quenching of chlorophyll fluorescence. 2. Isolated light-harvesting complexes.

The chlorophyll fluorescence yield of purified photosystem II light-harvesting complexes can be lowered by manipulation of experimental conditions. In several important respects, this quenching resembles the nonphotochemical quenching observed in isolated chloroplasts and leaves, therefore providing a model system for investigating the underlying mechanism. A methodology based on the principles of enzyme kinetic analysis has already been applied to isolated chloroplasts, and this same experimental approach was used here with purified LHCIIb, CP26, and CP29. It was found that the kinetics of the decrease in fluorescence yield robustly fitted a second-order kinetic model with respect to time after induction of quenching. The second-order rate constant was dependent upon the complex that was analyzed, the detergent concentration, the solution pH, and the presence of exogenous xanthophyll cycle carotenoids. In contrast, the formation of an absorbance change at 683 nm that accompanies quenching displayed first-order kinetics. The reversal of quenching also displayed second-order kinetics. These data show that quenching results from a binary reaction, possibly arising between two chlorophyll molecules. On the basis of these data, a model for the regulation of nonphotochemical quenching based upon the allosteric control of the conformation of light-harvesting complexes by protonation and xanthophyll binding is presented.

Kinetic analysis of nonphotochemical quenching of chlorophyll fluorescence. 1. Isolated chloroplasts.

Nonphotochemical quenching of chlorophyll fluorescence in plants is indicative of a process that dissipates excess excitation energy from the light-harvesting antenna of photosystem II. The major fraction of quenching is obligatorily dependent upon the thylakoid DeltapH and is regulated by the de-epoxidation state of the xanthophyll cycle carotenoids associated with the light-harvesting complexes. Basic principles of enzyme kinetics have been used to investigate this process in isolated chloroplasts. The extent of quenching was titrated against the estimated thylakoid lumen pH, and a sigmoidal relationship was obtained with a Hill coefficient of 4.5 and a pK of 4.7. Upon de-epoxidation, these parameters changed to 1.6 and 5.7, respectively. Antimycin A suppressed quenching, increasing the Hill coefficient and reducing the pK. The rate of induction of quenching fitted second-order kinetics with respect to illumination time, and the rate constant was dependent upon the DeltapH, the de-epoxidation state, the presence of antimycin, and also the presence of dibucaine, a quenching enhancer. All these data are consistent with the notion that quenching is caused by a conformational transition in a chloroplast thylakoid protein; this transition shows cooperativity with respect to proton binding, and is controlled by de-epoxidation state and various exogenous reagents.

Increasing rice photosynthesis by manipulation of the acclimation and adaptation to light.

There are three important considerations in assessing the interaction of crop plants with light: (a) how does the plant respond to the light environment both in the short-term (regulation) and in the long-term (acclimation), (b) under what conditions are these responses inadequate, leading to photoinhibition, and (c) are the responses optimally adapted for maximum agricultural yield? Despite a wealth of knowledge about these processes in model plant species, it is impossible to predict how significant they are in influencing the yield of rice. Therefore, in collaboration with IRRI, we have undertaken a study of photoinhibition and photoacclimation of rice under field conditions. The results of this study are presented, along with an assessment of the implications for improvement of rice yield.

Configuration and dynamics of xanthophylls in light-harvesting antennae of higher plants. Spectroscopic analysis of isolated light-harvesting complex of photosystem II and thylakoid membranes.

Resonance Raman excitation spectroscopy combined with ultra low temperature absorption spectral analysis of the major xanthophylls of higher plants in isolated antenna and intact thylakoid membranes was used to identify carotenoid absorption regions and study their molecular configuration. The major electronic transitions of the light-harvesting complex of photosystem II (LHCIIb) xanthophylls have been identified for both the monomeric and trimeric states of the complex. One long wavelength state of lutein with a 0-0 transition at 510 nm was detected in LHCIIb trimers. The short wavelength 0-0 transitions of lutein and neoxanthin were located at 495 and 486 nm, respectively. In monomeric LHCIIb, both luteins absorb around 495 nm, but slight differences in their protein environments give rise to a broadening of this band. The resonance Raman spectra of violaxanthin and zeaxanthin in intact thylakoid membranes was determined. The broad 0-0 absorption transition for zeaxanthin was found to be located in the 503-511 nm region. Violaxanthin exhibited heterogeneity, having two populations with one absorbing at 497 nm (0-0), 460 nm (0-1), and 429 nm (0-2), and the other major pool absorbing at 488 nm (0-0), 452 nm (0-1), and 423 nm (0-2). The origin of this heterogeneity is discussed. The configuration of zeaxanthin and violaxanthin in thylakoid membranes was different from that of free pigments, and both xanthophylls (notably, zeaxanthin) were found to be well coordinated within the antenna proteins in vivo, arguing against the possibility of their free diffusion in the membrane and supporting our recent biochemical evidence of their association with intact oligomeric light-harvesting complexes (Ruban, A. V., Lee, P. J., Wentworth, M., Young, A. J., and Horton, P. (1999) J. Biol. Chem. 274, 10458-10465).

Extensive developmental and metabolic alterations in cybrids Nicotiana tabacum (+ Hyoscyamus niger) are caused by complex nucleo-cytoplasmic incompatibility.

The genetic basis of multiple phenotypic alterations was studied in cell-engineered cybrids Nicotiana tabacum (+ Hyoscyamus niger) combining the nuclear genome of N. tabacum, plastome of H. niger and recombinant mitochondria. The plants possess a complex, maternally inheritable syndrome of nucleo-cytoplasmic incompatibility, severely affecting growth, metabolism and development. In vivo, the syndrome was manifested as: late germination of seeds; dramatic decrease of chlorophyll and carotenoids in cotyledons and leaves; altered morphology of cotyledons, leaves and flowers; and dwarfism. The leaf phenotype depended on light intensity. In 'green flowers' (an extreme phenotype), homeotic function B was downregulated. In vitro, the incompatibility syndrome was restricted to the pigment deficiency of cotyledons. Electron microscopy revealed perturbations in the differentiation of chloroplasts and palisade parenchyma cells in bleached leaves. The pigment deficiency accompanied by retarded growth is discussed as a result of plastome-genome incompatibility, whereas other features are likely to be due to nucleo-mitochondrial incompatibilities.