Sirine C. Fakra

Bio: Sirine C. Fakra is an academic researcher from Lawrence Berkeley National Laboratory. The author has contributed to research in topics: Hyperaccumulator & Stanleya pinnata. The author has an hindex of 45, co-authored 119 publications receiving 7339 citations.

Comet 81P/Wild 2 under a microscope.

Abstract: The Stardust spacecraft collected thousands of particles from comet 81P/Wild 2 and returned them to Earth for laboratory study. The preliminary examination of these samples shows that the nonvolatile portion of the comet is an unequilibrated assortment of materials that have both presolar and solar system origin. The comet contains an abundance of silicate grains that are much larger than predictions of interstellar grain models, and many of these are high-temperature minerals that appear to have formed in the inner regions of the solar nebula. Their presence in a comet proves that the formation of the solar system included mixing on the grandest scales.

Interferometer‐controlled scanning transmission X‐ray microscopes at the Advanced Light Source

Abstract: Two new soft X-ray scanning transmission microscopes located at the Advanced Light Source (ALS) have been designed, built and commissioned. Interferometer control implemented in both microscopes allows the precise measurement of the transverse position of the zone plate relative to the sample. Long-term positional stability and compensation for transverse displacement during translations of the zone plate have been achieved. The interferometer also provides low-distortion orthogonal x, y imaging. Two different control systems have been developed: a digital control system using standard VXI components at beamline 7.0, and a custom feedback system based on PC AT boards at beamline 5.3.2. Both microscopes are diffraction limited with the resolution set by the quality of the zone plates. Periodic features with 30 nm half period can be resolved with a zone plate that has a 40 nm outermost zone width. One microscope is operating at an undulator beamline (7.0), while the other is operating at a novel dedicated bending-magnet beamline (5.3.2), which is designed specifically to illuminate the microscope. The undulator beamline provides count rates of the order of tens of MHz at high-energy resolution with photon energies of up to about 1000 eV. Although the brightness of a bending-magnet source is about four orders of magnitude smaller than that of an undulator source, photon statistics limited operation with intensities in excess of 3 MHz has been achieved at high energy resolution and high spatial resolution. The design and performance of these microscopes are described.

Microbial polysaccharides template assembly of nanocrystal fibers.

Abstract: Biological systems can produce extraordinary inorganic structures and morphologies. The mechanisms of synthesis are poorly understood but are of great interest for engineering novel materials. We use spectromicroscopy to show that microbially generated submicrometer-diameter iron oxyhydroxide (FeOOH) filaments contain polysaccharides, providing an explanation for the formation of akaganeite pseudo–single crystals with aspect ratios of ∼1000:1. We infer that the cells extrude the polysaccharide strands to localize FeOOH precipitation in proximity to the cell membrane to harness the proton gradient for energy generation. Characterization of organic compounds with high spatial resolution, correlated with mineralogical information, should improve our understanding of biomineralization mechanisms.

Lithotrophic iron-oxidizing bacteria produce organic stalks to control mineral growth: implications for biosignature formation

Abstract: Neutrophilic Fe-oxidizing bacteria (FeOB) are often identified by their distinctive morphologies, such as the extracellular twisted ribbon-like stalks formed by Gallionella ferruginea or Mariprofundus ferrooxydans. Similar filaments preserved in silica are often identified as FeOB fossils in rocks. Although it is assumed that twisted iron stalks are indicative of FeOB, the stalk's metabolic role has not been established. To this end, we studied the marine FeOB M. ferrooxydans by light, X-ray and electron microscopy. Using time-lapse light microscopy, we observed cells excreting stalks during growth (averaging 2.2 μm h−1). Scanning transmission X-ray microscopy and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy show that stalks are Fe(III)-rich, whereas cells are low in Fe. Transmission electron microscopy reveals that stalks are composed of several fibrils, which contain few-nanometer-sized iron oxyhydroxide crystals. Lepidocrocite crystals that nucleated on the fibril surface are much larger (∼100 nm), suggesting that mineral growth within fibrils is retarded, relative to sites surrounding fibrils. C and N 1s NEXAFS spectroscopy and fluorescence probing show that stalks primarily contain carboxyl-rich polysaccharides. On the basis of these results, we suggest a physiological model for Fe oxidation in which cells excrete oxidized Fe bound to organic polymers. These organic molecules retard mineral growth, preventing cell encrustation. This model describes an essential role for stalk formation in FeOB growth. We suggest that stalk-like morphologies observed in modern and ancient samples may be correlated confidently with the Fe-oxidizing metabolism as a robust biosignature.

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Aggregation and morphology control enables multiple cases of high-efficiency polymer solar cells.

Abstract: Although the field of polymer solar cell has seen much progress in device performance in the past few years, several limitations are holding back its further development For instance, current high-efficiency (>90%) cells are restricted to material combinations that are based on limited donor polymers and only one specific fullerene acceptor Here we report the achievement of high-performance (efficiencies up to 108%, fill factors up to 77%) thick-film polymer solar cells for multiple polymer:fullerene combinations via the formation of a near-ideal polymer:fullerene morphology that contains highly crystalline yet reasonably small polymer domains This morphology is controlled by the temperature-dependent aggregation behaviour of the donor polymers and is insensitive to the choice of fullerenes The uncovered aggregation and design rules yield three high-efficiency (>10%) donor polymers and will allow further synthetic advances and matching of both the polymer and fullerene materials, potentially leading to significantly improved performance and increased design flexibility

Metal Catalysts for Heterogeneous Catalysis: From Single Atoms to Nanoclusters and Nanoparticles.

Abstract: Metal species with different size (single atoms, nanoclusters, and nanoparticles) show different catalytic behavior for various heterogeneous catalytic reactions. It has been shown in the literature that many factors including the particle size, shape, chemical composition, metal–support interaction, and metal–reactant/solvent interaction can have significant influences on the catalytic properties of metal catalysts. The recent developments of well-controlled synthesis methodologies and advanced characterization tools allow one to correlate the relationships at the molecular level. In this Review, the electronic and geometric structures of single atoms, nanoclusters, and nanoparticles will be discussed. Furthermore, we will summarize the catalytic applications of single atoms, nanoclusters, and nanoparticles for different types of reactions, including CO oxidation, selective oxidation, selective hydrogenation, organic reactions, electrocatalytic, and photocatalytic reactions. We will compare the results o...

Heavy metals in soils : trace metals and metalloids in soils and their bioavailability

Abstract: Preface.- Contributors.- List of Abbreviations.- Section 1: Basic Principles: Introduction.-Sources of Heavy Metals and Metalloids in Soils.- Chemistry of Heavy Metals and Metalloids in Soils.- Methods for the Determination of Heavy Metals and Metalloids in Soils.- Effects of Heavy Metals and Metalloids on Soil Organisms.- Soil-Plant Relationships of Heavy Metals and Metalloids.- Heavy Metals and Metalloids as Micronutrients for Plants and Animals.-Critical Loads of Heavy Metals for Soils.- Section 2: Key Heavy Metals And Metalloids: Arsenic.- Cadmium.- Chromium and Nickel.- Cobalt and Manganese.- Copper.-Lead.- Mercury.- Selenium.- Zinc.- Section 3: Other Heavy Metals And Metalloids Of Potential Environmental Significance: Antimony.- Barium.- Gold.- Molybdenum.- Silver.- Thallium.- Tin.- Tungsten.- Uranium.- Vanadium.- Glossary of Specialized Terms.- Index.