Growth of crystals in optical tweezers

We report here on the use of optical tweezers in the growth and manipulation of protein and inorganic crystals. Sodium chloride and hen egg-white lysozyme crystals were grown in a batch process, and then seeds from the solution were introduced into the optical tweezers. The regular and controllable shape and the known optical birefringence in these structures allowed a detailed study of the orientation effects in the beam due to both polarization and gradient forces. Additionally, we determined that the laser tweezers could be used to suspend a crystal for three-dimensional growth under varying conditions. Studies included increasing the protein concentration, thermal cycling, and a diffusion-induced increase in precipitant concentration. Preliminary studies on the use of the tweezers to create a localized seed for growth from polyethylene oxide solutions are also reported.

Growth of ultrananocrystalline diamond film by DC Arcjet plasma enhanced chemical vapor deposition

Self-standing diamond films were grown by DC Arcjet plasma enhanced chemical vapor deposition (CVD). The feed gasses were Ar/H 2/CH 4, in which the flow ratio of CH 4 to H 2 (FCH4/FH2) was varied from 5% to 20%. Two distinct morphologies were observed by scanning electron microscope (SEM), i.e. the pineapple-like morphology and the cauliflower-like morphology. It was found that the morphologies of the as-grown films are strongly dependent on the flow ratio of CH 4 to H 2 in the feed gasses. High resolution transmission electron microscope (HRTEM) survey results revealed that there were nanocrystalline grains within the pineapple-like films whilst there were ultrananocrystalline grains within cauliflower-like films. X-ray diffraction (XRD) results suggested that (110) crystalline plane was the dominant surface in the cauliflower-like films whilst (100) crystalline plane was the dominant surface in the pineapple-like films. Raman spectroscopy revealed that nanostructured carbon features could be observed in both types of films. Plasma diagnosis was carried out in order to understand the morphology dependent growth mechanism. It could be concluded that the film morphology was strongly influenced by the density of gas phases. The gradient of C2 radical was found to be different along the growth direction under the different growth conditions. © 2012 Elsevier B.V. All rights reserved.

Life cycle of Deccan trap magma chambers: A crystal scale elemental and strontium isotopic investigation

The Deccan Trap basalts are the remnants of a massive series of lava flows that erupted at the K/T boundary and covered 1-2 million km2 of west-central India. This eruptive event is of global interest because of its possible link to the major mass extinction event, and there is much debate about the duration of this massive volcanic event. In contrast to isotopic or paleomagnetic dating methods, I explore an alternative approach to determine the lifecycle of the magma chambers that supplied the lavas, and extend the concept to obtain a tighter constraint on Deccan’s duration. My method relies on extracting time information from elemental and isotopic diffusion across zone boundaries in individual crystals. I determined elemental and Sr-isotopic variations across abnormally large (2-5 cm) plagioclase crystals from the Thalghat and Kashele “Giant Plagioclase Basalts” from the lowermost Jawhar and Igatpuri Formations respectively in the thickest Western Ghats section near Mumbai. I also obtained bulk rock major, trace and rare earth element chemistry of each lava flow from the two formations. Thalghat flows contain only 12% zoned crystals, with 87 Sr/86Sr ratios of 0.7096 in the core and 0.7106 in the rim, separated by a sharp boundary. In contrast, all Kashele crystals have a wider range of 87Sr/86Sr values, with multiple zones. Geochemical modeling of the data suggests that the two types of crystals grew in distinct magmatic environments. Modeling intracrystalline diffusive equilibration between the core and rim of Thalghat crystals led me to obtain a crystal growth rate of 2.03x10-10 cm/s and a residence time of 780 years for the crystals in the magma chamber(s). Employing some assumptions based on field and geochronologic evidence, I extrapolated this residence time to the entire Western Ghats and obtained an estimate of 25,000–35,000 years for the duration of Western Ghats volcanism. This gave an eruptive rate of 30–40 km3/yr, which is much higher than any presently erupting volcano. This result will remain speculative until a similarly detailed analytical-modeling study is performed for the rest of the Western Ghats formations.

Multi-impurity adsorption model for modeling crystal purity and shape evolution during crystallization processes in impure media

Peer reviewed

On the microstructure, growth pattern and original porosity of belemnite rostra: insights from calcitic Jurassic belemnites

Calcitic belemnite rostra are usually employed to perform paleoenvironmental studies based on geochemical data. However, several questions, such as their original porosity and microstructure, remain open, despite they are essential to make accurate interpretations based on geochemical analyses.This paper revisits and enlightens some of these questions. Petrographic data demonstrate that calcite crystals of the rostrum solidum of belemnites grow from spherulites that successively develop along the apical line, resulting in a “regular spherulithic prismatic” microstructure. Radially arranged calcite crystals emerge and diverge from the spherulites: towards the apex, crystals grow until a new spherulite is formed; towards the external walls of the rostrum, the crystals become progressively bigger and prismatic. Adjacent crystals slightly vary in their c-axis orientation, resulting in undulose extinction. Concentric growth layering develops at different scales and is superimposed and traversed by a radial pattern, which results in the micro-fibrous texture that is observed in the calcite crystals in the rostra.Petrographic data demonstrate that single calcite crystals in the rostra have a composite nature, which strongly suggests that the belemnite rostra were originally porous. Single crystals consistently comprise two distinct zones or sectors in optical continuity: 1) the inner zone is fluorescent, has relatively low optical relief under transmitted light (TL) microscopy, a dark-grey color under backscatter electron microscopy (BSEM), a commonly triangular shape, a “patchy” appearance and relatively high Mg and Na contents; 2) the outer sector is non-fluorescent, has relatively high optical relief under TL, a light-grey color under BSEM and low Mg and Na contents. The inner and fluorescent sectors are interpreted to have formed first as a product of biologically controlled mineralization during belemnite skeletal growth and the non-fluorescent outer sectors as overgrowths of the former, filling the intra- and inter-crystalline porosity. This question has important implications for making paleoenvironmental and/or paleoclimatic interpretations based on geochemical analyses of belemnite rostra.Finally, the petrographic features of composite calcite crystals in the rostra also suggest the non-classical crystallization of belemnite rostra, as previously suggested by other authors.

Multiscale Modeling and Simulation of Stepped Crystal Surfaces

A primary goal of this dissertation is to understand the links between mathematical models that describe crystal surfaces at three fundamental length scales: The scale of individual atoms, the scale of collections of atoms forming crystal defects, and macroscopic scale. Characterizing connections between different classes of models is a critical task for gaining insight into the physics they describe, a long-standing objective in applied analysis, and also highly relevant in engineering applications. The key concept I use in each problem addressed in this thesis is coarse graining, which is a strategy for connecting fine representations or models with coarser representations. Often this idea is invoked to reduce a large discrete system to an appropriate continuum description, e.g. individual particles are represented by a continuous density. While there is no general theory of coarse graining, one closely related mathematical approach is asymptotic analysis, i.e. the description of limiting behavior as some parameter becomes very large or very small. In the case of crystalline solids, it is natural to consider cases where the number of particles is large or where the lattice spacing is small. Limits such as these often make explicit the nature of links between models capturing different scales, and, once established, provide a means of improving our understanding, or the models themselves. Finding appropriate variables whose limits illustrate the important connections between models is no easy task, however. This is one area where computer simulation is extremely helpful, as it allows us to see the results of complex dynamics and gather clues regarding the roles of different physical quantities. On the other hand, connections between models enable the development of novel multiscale computational schemes, so understanding can assist computation and vice versa. Some of these ideas are demonstrated in this thesis. The important outcomes of this thesis include: (1) a systematic derivation of the step-flow model of Burton, Cabrera, and Frank, with corrections, from an atomistic solid-on-solid-type models in 1+1 dimensions; (2) the inclusion of an atomistically motivated transport mechanism in an island dynamics model allowing for a more detailed account of mound evolution; and (3) the development of a hybrid discrete-continuum scheme for simulating the relaxation of a faceted crystal mound. Central to all of these modeling and simulation efforts is the presence of steps composed of individual layers of atoms on vicinal crystal surfaces. Consequently, a recurring theme in this research is the observation that mesoscale defects play a crucial role in crystal morphological evolution.

Correlation among Growth Conditions, Morphology, and Optical Properties of Nanocolumnar InGaN/GaN Heterostructures Selectively Grown by Molecular Beam Epitaxy

This work reports on the selective area growth mechanism of green-emitting InGaN/GaN nanocolumns. The evolution of the morphology of the InGaN segment is found to depend critically on the nominal III/V ratio as well as the diameter of the GaN section. In addition, the In distribution inside the InGaN segment is found to depend on the local III/V and In/Ga ratios.

Life Cycle of Deccan Trap Magma Chambers: A Crystal Scale Elemental and Strontium Isotopic Investigation

The Deccan Trap basalts are the remnants of a massive series of lava flows that erupted at the K/T boundary and covered 1-2 million km2 of west-central India. This eruptive event is of global interest because of its possible link to the major mass extinction event, and there is much debate about the duration of this massive volcanic event. In contrast to isotopic or paleomagnetic dating methods, I explore an alternative approach to determine the lifecycle of the magma chambers that supplied the lavas, and extend the concept to obtain a tighter constraint on Deccan’s duration. My method relies on extracting time information from elemental and isotopic diffusion across zone boundary in an individual crystal. I determined elemental and Sr-isotopic variations across abnormally large (2-5 cm) plagioclase crystals from the Thalghat and Kashele “Giant Plagioclase Basalts” from the lowermost Jawhar and Igatpuri Formations respectively in the thickest Western Ghats section near Mumbai. I also obtained bulk rock major, trace and rare earth element chemistry of each lava flow from the two formations. Thalghat flows contain only 12% zoned crystals, with 87Sr/86Sr ratios of 0.7096 in the core and 0.7106 in the rim, separated by a sharp boundary. In contrast, all Kashele crystals have a wider range of 87Sr/86Sr values, with multiple zones. Geochemical modeling of the data suggests that the two types of crystals grew in distinct magmatic environments. Modeling intracrystalline diffusive equilibration between the core and rim of Thalghat crystals led me to obtain a crystal growth rate of 2.03x10-10 cm/s and a residence time of 780 years for the crystals in the magma chamber(s). Employing some assumptions based on field and geochronologic evidence, I extrapolated this residence time to the entire Western Ghats and obtained an estimate of 25,000 – 35,000 years for the duration of Western Ghats volcanism. This gave an eruptive rate of 30 – 40 km3/yr, which is much higher than any presently erupting volcano. This result will remain speculative until a similarly detailed analytical-modeling study is performed for the rest of the Western Ghats formations.

Sand bioconsolidation through the precipitation of calcium carbonate by two ureolytic bacteria

Two ureolytic strains, B. sphaericus LMG 22257 and Bacillus sp (I-001), were tested for their ability to consolidate sand by submitting them to two days` treatment using 10(7) viable cell concentrations of inocula and medium precipitation with calcium ions. The results showed that B. sphaericus LMG 22257 induced greater calcium carbonate formation. Both strains produced calcite and were able to consolidate sand. Tensile strength of consolidated sand was not a function of the amount of precipitated CaCO(3) but a linear function of the ratio bioconsolidation index (BC) defined as the ratio of CaCO(3) volume to initial sand porosity. A simple model to estimate the engineering benefits of consolidation is proposed. (C) 2011 Elsevier B.V. All rights reserved.

Macrosegregation of Impurities in Directionally Solidified Silicon

Directional solidification of molten metallurgical-grade Si was carried out in a vertical Bridgman furnace. The effects of changing the mold velocity from 5 to 110 mu m seconds(-1) on the macrosegregation of impurities during solidification were investigated. The macrostructures of the cylindrical Si ingots obtained in the experiments consist mostly of columnar grains parallel to the ingot axis. Because neither cells nor dendrites can be observed on ingot samples, the absence of precipitated particles and the fulfillment of the constitutional supercooling criterion suggest a planar solid-liquid interface for mold velocities a parts per thousand currency sign10 mu m seconds(-1). Concentration profiles of several impurities were measured along the ingots, showing that their bottom and middle are purer than the metallurgical Si from which they solidified. At the ingot top, however, impurities accumulated, indicating the typical normal macrosegregation. When the mold velocity decreases, the macrosegregation and ingot purity increase, changing abruptly for a velocity variation from 20 to 10 mu m seconds(-1). A mathematical model of solute transport during solidification shows that, for mold velocities a parts per thousand yen20 mu m seconds(-1), macrosegregation is caused mainly by diffusion in a stagnant liquid layer assumed at the solid-liquid interface, whereas for lower velocities, macrosegregation increases as a result of more intense convective solute transport.

Adhesion of microbes using 3-aminopropyl triethoxy silane and specimen stabilisation techniques for analytical transmission electron microscopy

A variety of adhesive support-films were tested for their ability to adhere various biological specimens for transmission electron microscopy. Support films primed with 3-amino-propyl triethoxy silane (APTES), poly-L-lysine, carbon and ultraviolet-B (UV-B)-irradiated carbon were tested for their ability to adhere a variety of biological specimens including axenic cultures of Bacillus subtilis and Escherichia coli and wild-type magnetotactic bacteria. The effects of UV-B irradiation on the support film in the presence of air and electrostatic charge on primer deposition were tested and the stability of adhered specimens on various surfaces was also compared. APTES-primed UV-B-irradiated Pioloform(TM) was consistently the best adhesive, especially for large cells, and when adhered specimens were UV-B irradiated they became remarkably stable under an electron beam. This assisted the acquisition of in situ phase-contrast lattice images from a variety of biominerals in magnetotactic bacteria, in particular metastable greigite magnetosomes. Washing tests indicated that specimens adhering to APTES-primed UV-B-irradiated Pioloform(TM) were covalently coupled. The electron beam stability was hypothesised to be the result of mechanical strengthening of the specimen and support film and the reduced electrical resistance in the specimen and support film due to their polymerization and covalent coupling.