Erratum: Improved real-space genetic algorithm for crystal structure and polymorph prediction [Phys. Rev. B 77, 134117 (2008)]

In our earlier work, there was an error in the derivation of the spherically averaged scattering intensity, presented as Eq. (5) in the original paper. This equation should have readΛ(kr)=∑n=1Nρ′(n)2+2∑n=1N∑m>nNρ′(n)ρ′(m)j0(kr∣∣∣∣rn−rm|), (5)where j0(r) is the spherical Bessel function of the first kind

Nutritional response of a coccolithophore to changing pH and temperature

Unidad de excelencia María de Maeztu CEX2019-000940-MAcord transformatiu CRUE-CSICCoccolithophores are a calcifying unicellular phytoplankton group that are at the base of the marine food web, and their lipid content provides a source of energy to consumers. Coccolithophores are vulnerable to ocean acidification and warming, therefore it is critical to establish the effects of climate change on these significant marine primary producers, and determine potential consequences that these changes can have on their consumers. Here, we quantified the impact of changes in pH and temperature on the nutritional condition (lipid content, particulate organic carbon/nitrogen), growth rate, and morphology of the most abundant living coccolithophore species, Emiliania huxleyi. We used a regression type approach with nine pH levels (ranging from 7.66 to 8.44) and two temperatures (15°C and 20°C). Lipid production was greater under reduced pH, and growth rates were distinctly lower at 15°C than at 20°C. The production potential of lipids, which estimates the availability of lipids to consumers, increased under 20°C, but decreased under low pH. The results indicate that, while consumers will benefit energetically under ocean warming, this benefit will be mitigated by ocean acidification. The carbon to nitrogen ratio was higher at 20°C and low pH, indicating that the nutritional quality of coccolithophores for consumers will decline under climate change. The impact of low pH on the structural integrity of the coccosphere may also mean that coccolithophores are easier to digest for consumers. Many responses suggest cellular stress, indicating that increases in temperature and reductions in pH may have a negative impact on the ecophysiology of coccolithophores

Quantum diffusion of H/D on Ni(111)—A partially adiabatic centroid MD study

We present the results of a theoretical study of H/D diffusion on a Ni(111) surface at a range of temperatures, from 250 K to 75 K. The diffusion is studied using both classical molecular dynamics and the partially adiabatic centroid molecular dynamics method. The calculations are performed with the hydrogen (or deuterium) moving in 3D across a static nickel surface using a novel Fourier interpolated potential energy surface which has been parameterized to density functional theory calculations. The results of the classical simulations are that the calculated diffusion coefficients are far too small and with too large a variation with temperature compared with experiment. By contrast, the quantum simulations are in much better agreement with experiment and show that quantum effects in the diffusion of hydrogen are significant at all temperatures studied. There is also a crossover to a quantum-dominated diffusive regime for temperatures below ∼150 K for hydrogen and ∼85 K for deuterium. The quantum diffusion coefficients are found to accurately reproduce the spread in values with temperature, but with an absolute value that is a little high compared with experiment

DL_MG : A Parallel Multigrid Poisson and Poisson–Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution

The solution of the Poisson equation is a crucial step in electronic structure calculations, yielding the electrostatic potential—a key component of the quantum mechanical Hamiltonian. In recent decades, theoretical advances and increases in computer performance have made it possible to simulate the electronic structure of extended systems in complex environments. This requires the solution of more complicated variants of the Poisson equation, featuring nonhomogeneous dielectric permittivities, ionic concentrations with nonlinear dependencies, and diverse boundary conditions. The analytic solutions generally used to solve the Poisson equation in vacuum (or with homogeneous permittivity) are not applicable in these circumstances, and numerical methods must be used. In this work, we present DL_MG, a flexible, scalable, and accurate solver library, developed specifically to tackle the challenges of solving the Poisson equation in modern large-scale electronic structure calculations on parallel computers. Our solver is based on the multigrid approach and uses an iterative high-order defect correction method to improve the accuracy of solutions. Using two chemically relevant model systems, we tested the accuracy and computational performance of DL_MG when solving the generalized Poisson and Poisson–Boltzmann equations, demonstrating excellent agreement with analytic solutions and efficient scaling to ∼10^9 unknowns and 100s of CPU cores. We also applied DL_MG in actual large-scale electronic structure calculations, using the ONETEP linear-scaling electronic structure package to study a 2615 atom protein–ligand complex with routinely available computational resources. In these calculations, the overall execution time with DL_MG was not significantly greater than the time required for calculations using a conventional FFT-based solver

Simultaneous Prediction of the Magnetic and Crystal Structure of Materials Using a Genetic Algorithm

We introduce a number of extensions and enhancements to a genetic algorithm for crystal structure prediction, to make it suitable to study magnetic systems. The coupling between magnetic properties and crystal structure means that it is essential to take a holistic approach, and we present for the first time, a genetic algorithm that performs a simultaneous global optimisation of both magnetic structure and crystal structure. We first illustrate the power of this approach on a novel test system—the magnetic Lennard–Jones potential—which we define. Then we study the complex interface structures found at the junction of a Heusler alloy and a semiconductor substrate as found in a proposed spintronic device and show the impact of the magnetic interface structure on the device performance

Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell

International audienceBackground: Eukaryotes are classified as either haplontic, diplontic, or haplo-diplontic, depending on which ploidy levels undergo mitotic cell division in the life cycle. Emiliania huxleyi is one of the most abundant phytoplankton species in the ocean, playing an important role in global carbon fluxes, and represents haptophytes, an enigmatic group of unicellular organisms that diverged early in eukaryotic evolution. This species is haplo-diplontic. Little is known about the haploid cells, but they have been hypothesized to allow persistence of the species between the yearly blooms of diploid cells. We sequenced over 38,000 expressed sequence tags from haploid and diploid E. huxleyi normalized cDNA libraries to identify genes involved in important processes specific to each life phase (2N calcification or 1N motility), and to better understand the haploid phase of this prominent haplo-diplontic organism. Results: The haploid and diploid transcriptomes showed a dramatic differentiation, with approximately 20% greater transcriptome richness in diploid cells than in haploid cells and only <= 50% of transcripts estimated to be common between the two phases. The major functional category of transcripts differentiating haploids included signal transduction and motility genes. Diploid-specific transcripts included Ca(2+), H(+), and HCO(3)(-) pumps. Potential factors differentiating the transcriptomes included haploid-specific Myb transcription factor homologs and an unusual diploid-specific histone H4 homolog. Conclusions: This study permitted the identification of genes likely involved in diploid-specific biomineralization, haploid-specific motility, and transcriptional control. Greater transcriptome richness in diploid cells suggests they may be more versatile for exploiting a diversity of rich environments whereas haploid cells are intrinsically more streamlined

A phylogenetic mosaic plastid proteome and unusual plastid-targeting signals in the green-colored dinoflagellate Lepidodinium chlorophorum

Background Plastid replacements through secondary endosymbioses include massive transfer of genes from the endosymbiont to the host nucleus and require a new targeting system to enable transport of the plastid-targeted proteins across 3-4 plastid membranes. The dinoflagellates are the only eukaryotic lineage that has been shown to have undergone several plastid replacement events, and this group is thus highly relevant for studying the processes involved in plastid evolution. In this study, we analyzed the phylogenetic origin and N-terminal extensions of plastid-targeted proteins from Lepidodinium chlorophorum, a member of the only dinoflagellate genus that harbors a green secondary plastid rather than the red algal-derived, peridinin-containing plastid usually found in photosynthetic dinoflagellates. Results We sequenced 4,746 randomly picked clones from a L. chlorophorum cDNA library. 22 of the assembled genes were identified as genes encoding proteins functioning in plastids. Some of these were of green algal origin. This confirms that genes have been transferred from the plastid to the host nucleus of L. chlorophorum and indicates that the plastid is fully integrated as an organelle in the host. Other nuclear-encoded plastid-targeted protein genes, however, are clearly not of green algal origin, but have been derived from a number of different algal groups, including dinoflagellates, streptophytes, heterokonts, and red algae. The characteristics of N-terminal plastid-targeting peptides of all of these genes are substantially different from those found in peridinin-containing dinoflagellates and green algae. Conclusions L. chlorophorum expresses plastid-targeted proteins with a range of different origins, which probably arose through endosymbiotic gene transfer (EGT) and horizontal gene transfer (HGT). The N-terminal extension of the genes is different from the extensions found in green alga and other dinoflagellates (peridinin- and haptophyte plastids). These modifications have likely enabled the mosaic proteome of L. chlorophorum