Study of the volume and spin collapse in orthoferrite LuFeO_3 using LDA+U

Rare earth (R) orthoferrites RFeO_3 exhibit large volume transitions associated with a spin collapse. We present here ab initio calculations on LuFeO_3. We show that taking into account the strong correlation among the Fe-3d electrons is necessary. Indeed, with the LDA+U method in the Projector Augmented Wave (PAW), we are able to describe the isostructural phase transition at 50 GPa, as well as a volume discontinuity of 6.0% at the transition and the considerable reduction of the magnetic moment on the Fe ions. We further investigate the effect of the variation of U and J and find a linear dependence of the transition pressure on these parameters. We give an interpretation for the non-intuitive effect of J. This emphasizes the need for a correct determination of these parameters especially when the LDA+U is applied to systems (e.g in geophysical investigations) where the transition pressure is a priori unknown

Virtual-crystal approximation that works: Locating a composition phase boundary in Pb(Zr_{1-x}Ti_3)O_3

We present a new method for modeling disordered solid solutions, based on the virtual crystal approximation (VCA). The VCA is a tractable way of studying configurationally disordered systems; traditionally, the potentials which represent atoms of two or more elements are averaged into a composite atomic potential. We have overcome significant shortcomings of the standard VCA by developing a potential which yields averaged atomic properties. We perform the VCA on a ferroelectric oxide, determining the energy differences between the high-temperature rhombohedral, low-temperature rhombohedral and tetragonal phases of Pb(Zr_{1-x}Ti_x)O_3 at x=0.5 and comparing these results to superlattice calculations and experiment. We then use our new method to determine the preferred structural phase at x=0.4. We find that the low-temperature rhombohedral phase becomes the ground state at x=0.4, in agreement with experimental findings.Comment: 5 pages, no figure

THERMAL DENATURATION OF MONOMERIC AND TRIMERIC PHYCOCYANINS STUDIED BY STATIC AND SPECTROSCOPY POLARIZED TIME-RESOLVED FLUORESCENCE

C-Phycocyanin (PC) and allophycocyanin (APC). as well as the a-subunit of PC. have been isolated from the blue-green alga (cyanobacterium). Spirulina platensis. The effects of partial thermal denaturation of PC and of its state of aggregation have been studied by ps time-resolved, polarized fluorescence spectroscopy. All measurements have been performed under low photon fluxes (< 10’ ’ photonsipulse x cm’) to minimize singlet-singlet annihilation processes. A complex decay is obtained under most conditions, which can be fitted satisfactorily with a bi-exponential (7’ = 70400 ps. T? = 1000-3000 ps) for both the isotropic and the polarized part, but with different intensities and time constants for the two decay curves. The data are interpreted in the frameworkof the model first developed by Teak and Dale (Biochern. J. 116, 161 (1970)], which divides the spectroscopically different chromophores in (predominantly) sensitizing (s) and fluorescing U, ones. If one assumes temperature dependent losses in the energy transfer from the s to the f and between f chromophores. both the biexponential nature of the isotropic fluorescence decay and the polarization data can be rationalized. In the isotropic emission (corresponding to the population of excited states) the short lifetime is related to the s-,f transfer. the longer one to the “free“ decay of the final acceptor(s) (= f). The polarized part is dominated by an extremely short decay time. which is related to s+f transfer, as well as to resonance transfer between the f-chromophores

FLUORESCENCE AND CIRCULAR DICHROISM STUDIES ON THE PHYCOERYTHROCYANINS FROM THE CYANOBACTERIUM

Two phycoerythrocyanin (PEC) fractions have been obtained from the phycobilisomes of the cyanobac-terium Westiellopsis prolifica ARM 365. They have been characterized by absorption, fluorescence and circular dichroism spectroscopy. One of them is spectroscopically similar to a PEC trimer known from other organisms. Whereas efficient energy transfer from its violin (α-84) to the cyanin (β-84, 155) chromophores is efficient in the trimer (αβ it is impeded after dissociation to the monomer (α,β). A second fraction of PEC which we earlier termed PEC(X) (Maruthi Sai et al., Photochem. Photobiol. 55,119–124, 1992), exhibited the spectral properties similar to that of the α-subunit of PEC from Mastigocladus laminosus. With this highly photoactive fraction, the circular dichroism spectra of the violobilin chromophore in both photoreversible states were obtained

Synthetic biology and biomass conversion: a match made in heaven?

To move our economy onto a sustainable basis, it is essential that we find a replacement for fossil carbon as a source of liquid fuels and chemical industry feedstocks. Lignocellulosic biomass, available in enormous quantities, is the only feasible replacement. Many micro-organisms are capable of rapid and efficient degradation of biomass, employing a battery of specialized enzymes, but do not produce useful products. Attempts to transfer biomass-degrading capability to industrially useful organisms by heterologous expression of one or a few biomass-degrading enzymes have met with limited success. It seems probable that an effective biomass-degradation system requires the synergistic action of a large number of enzymes, the individual and collective actions of which are poorly understood. By offering the ability to combine any number of transgenes in a modular, combinatorial way, synthetic biology offers a new approach to elucidating the synergistic action of combinations of biomass-degrading enzymes in vivo and may ultimately lead to a transferable biomass-degradation system. Also, synthetic biology offers the potential for assembly of novel product-formation pathways, as well as mechanisms for increased solvent tolerance. Thus, synthetic biology may finally lead to cheap and effective processes for conversion of biomass to useful products

Redefining genomic privacy: trust and empowerment

Fulfilling the promise of the genetic revolution requires the analysis of large datasets containing information from thousands to millions of participants. However, sharing human genomic data requires protecting subjects from potential harm. Current models rely on de-identification techniques in which privacy versus data utility becomes a zero-sum game. Instead, we propose the use of trust-enabling techniques to create a solution in which researchers and participants both win. To do so we introduce three principles that facilitate trust in genetic research and outline one possible framework built upon those principles. Our hope is that such trust-centric frameworks provide a sustainable solution that reconciles genetic privacy with data sharing and facilitates genetic research

‘Ethnic group’, the state and the politics of representation

The assertion, even if only by implication, that ‘ethnic group’ categories represent ‘real’ tangible entities, indeed identities, is commonplace not only in the realms of political and policy discourse but also amongst contemporary social scientists. This paper, following Brubaker (2002), questions this position in a number of key respects: of these three issues will dominate the discussion that follows. First, there is an interrogation of the proposition that those to whom the categories/labels refer constitute sociologically meaningful ‘groups’ as distinct from (mere) human collectivities. Secondly, there is the question of how these categories emerge, i.e. exactly what series of events, negotiations and contestations lie behind their construction and social acceptance. Thirdly, and as a corollary to the latter point, we explore the process of reification that leads to these categories being seen to represent ‘real things in the world’ (ibid.)

Nonequilibrium effects in DNA microarrays: a multiplatform study

It has recently been shown that in some DNA microarrays the time needed to reach thermal equilibrium may largely exceed the typical experimental time, which is about 15h in standard protocols (Hooyberghs et al. Phys. Rev. E 81, 012901 (2010)). In this paper we discuss how this breakdown of thermodynamic equilibrium could be detected in microarray experiments without resorting to real time hybridization data, which are difficult to implement in standard experimental conditions. The method is based on the analysis of the distribution of fluorescence intensities I from different spots for probes carrying base mismatches. In thermal equilibrium and at sufficiently low concentrations, log I is expected to be linearly related to the hybridization free energy $\Delta G$ with a slope equal to $1/RT_{exp}$, where $T_{exp}$ is the experimental temperature and R is the gas constant. The breakdown of equilibrium results in the deviation from this law. A model for hybridization kinetics explaining the observed experimental behavior is discussed, the so-called 3-state model. It predicts that deviations from equilibrium yield a proportionality of $\log I$ to $\Delta G/RT_{eff}$. Here, $T_{eff}$ is an effective temperature, higher than the experimental one. This behavior is indeed observed in some experiments on Agilent arrays. We analyze experimental data from two other microarray platforms and discuss, on the basis of the results, the attainment of equilibrium in these cases. Interestingly, the same 3-state model predicts a (dynamical) saturation of the signal at values below the expected one at equilibrium.Comment: 27 pages, 9 figures, 1 tabl

FÖRSTER TRANSFER CALCULATIONS BASED ON CRYSTAL STRUCTURE DATA FROM Agmenellum quadruplicatum C-PHYCOCYANIN

Excitation energy transfer in C-phycocyanin is modeled using the Forster inductive resonance mechanism. Detailed calculations are carried out using coordinates and orientations of the chromophores derived from X-ray crystallographic studies of C-phycocyanin from two different species (Schirmer et al, J. Mol. Biol. 184, 257–277 (1985) and ibid., 188, 651-677 (1986)). Spectral overlap integrals are estimated from absorption and fluorescence spectra of C-phycocyanin of Mastigocladus laminosus and its separated subunits. Calculations are carried out for the β-subunit, αβ-monomer, (αβ)3-trimer and (αβ)0-hexamer species with the following chromophore assignments: β155 = 's’(sensitizer), β84 =‘f (fluorescer) and α84 =‘m’(intermediate):]:. The calculations show that excitation transfer relaxation occurs to 3=98% within 200 ps in nearly every case; however, the rates increase as much as 10-fold for the higher aggregates. Comparison with experimental data on fluorescence decay and depolarization kinetics from the literature shows qualitative agreement with these calculations. We conclude that Forster transfer is sufficient to account for all of the observed fluorescence properties of C-phycocyanin in aggregation states up to the hexamer and in the absence of linker polypeptides

Determination of the intrinsic ferroelectric polarization in orthorhombic HoMnO3

Whether large ferroelectric polarization P exists in the orthorhombic HoMnO3 with the E-type antiferromagnetic spin ordering or not remains as one of unresolved, challenging issues in the physics of multiferroics. The issue is closely linked to an intriguing experimental difficulty for determining P of polycrystalline specimens that conventional pyroelectric current measurements performed after a poling procedure under high dc electric fields are subject to large errors due to the problems caused by leakage currents or space charges. To overcome the difficulty, we employed the PUND method, which uses successively the two positive and two negative electrical pulses, to directly measure electrical hysteresis loops in several polycrystalline HoMnO3 specimens below their N\'eel temperatures. We found that all the HoMnO3 samples had similar remnant polarization Pr values at each temperature, regardless of their variations in resistivity, dielectric constant, and pyroelectric current levels. Moreover, Pr of ~0.07 \mu\C/cm2 at 6 K is consistent with the P value obtained from the pyroelectric current measurement performed after a short pulse poling. Our findings suggest that intrinsic P of polycrystalline HoMnO3 can be determined through the PUND method and P at 0 K may reach ~0.24 \mu\C/cm2 in a single crystalline specimen.Comment: 21 pages, 6 figures, submitted to New Journal of Physic