Direct observation of adsorption sites of protein impurities and their effects on step advancement of protein crystals

We measured noninvasively step velocities of elementary two-dimensional (2D) islands on {110} faces of tetragonal lysozyme crystals, under various supersaturations, by laser confocal microscopy combined with differential interference contrast microscopy. We studied the correlation between the effects of protein impurities on the growth of elementary steps and their adsorption sites on a crystal surface, using three kinds of proteins: fluorescent-labeled lysozyme (F-lysozyme), covalently bonded dimers of lysozyme (dimer), and a 18 kDa polypeptide (18 kDa). These three protein impurities suppressed the advancement of the steps. However, they exhibited different supersaturation dependencies of the suppression of the step velocities. To clarify the cause of this difference, we observed in situ the adsorption sites of individual molecules of F-lysozyme and fluorescent-labeled dimer (F-dimer) on the crystal surface by single-molecule visualization. We found that F-lysozyme adsorbed preferentially on steps (i.e., kinks), whereas F-dimer adsorbed randomly on terraces. Taking into account the different adsorption sites of F-lysozyme and F-dimer, we could successfully explain the different effects of the impurities on the step velocities. These observations strongly suggest that 18 kDa also adsorbs randomly on terraces. Seikagaku lysozyme exhibited a complex effect that could not alone be explained by the two major impurities (dimer and 18 kDa) present in Seikagaku lysozyme, indicating that trace amounts of other impurities significantly affect the step advancement.

Crystals that count! Physical principles and experimental investigations of DNA tile self-assembly

Algorithmic DNA tiles systems are fascinating. From a theoretical perspective, they can result in simple systems that assemble themselves into beautiful, complex structures through fundamental interactions and logical rules. As an experimental technique, they provide a promising method for programmably assembling complex, precise crystals that can grow to considerable size while retaining nanoscale resolution. In the journey from theoretical abstractions to experimental demonstrations, however, lie numerous challenges and complications.

In this thesis, to examine these challenges, we consider the physical principles behind DNA tile self-assembly. We survey recent progress in experimental algorithmic self-assembly, and explain the simple physical models behind this progress. Using direct observation of individual tile attachments and detachments with an atomic force microscope, we test some of the fundamental assumptions of the widely-used kinetic Tile Assembly Model, obtaining results that fit the model to within error. We then depart from the simplest form of that model, examining the effects of DNA sticky end sequence energetics on tile system behavior. We develop theoretical models, sequence assignment algorithms, and a software package, StickyDesign, for sticky end sequence design.

As a demonstration of a specific tile system, we design a binary counting ribbon that can accurately count from a programmable starting value and stop growing after overflowing, resulting in a single system that can construct ribbons of precise and programmable length. In the process of designing the system, we explain numerous considerations that provide insight into more general tile system design, particularly with regards to tile concentrations, facet nucleation, the construction of finite assemblies, and design beyond the abstract Tile Assembly Model.

Finally, we present our crystals that count: experimental results with our binary counting system that represent a significant improvement in the accuracy of experimental algorithmic self-assembly, including crystals that count perfectly with 5 bits from 0 to 31. We show some preliminary experimental results on the construction of our capping system to stop growth after counters overflow, and offer some speculation on potential future directions of the field.

I. Electronic states of heavily-doped molecular crystals--naphthalene. I. Theoretical. II. Experimental. II. Lowest singlet and triplet excited states of pyrazine

PART I

The energy spectrum of heavily-doped molecular crystals was treated in the Green’s function formulation. The mixed crystal Green’s function was obtained by averaging over all possible impurity distributions. The resulting Green’s function, which takes the form of an infinite perturbation expansion, was further approximated by a closed form suitable for numerical calculations. The density-of-states functions and optical spectra for binary mixtures of normal naphthalene and deuterated naphthalene were calculated using the pure crystal density-of-state functions. The results showed that when the trap depth is large, two separate energy bands persist, but when the trap depth is small only a single band exists. Furthermore, in the former case it was found that the intensities of the outer Davydov bands are enhanced whereas the inner bands are weakened. Comparisons with previous theoretical calculations and experimental results are also made.

PART II

The energy states and optical spectra of heavily-doped mixed crystals are investigated. Studies are made for the following binary systems: (1) naphthalene-h₈ and d₈, (2) naphthalene--h₈ and αd₄, and (3) naphthalene--h₈ and βd₁, corresponding to strong, medium and weak perturbations. In addition to ordinary absorption spectra at 4˚K, band-to-band transitions at both 4˚K and 77˚K are also analyzed with emphasis on their relations to cooperative excitation and overall density-of-states functions for mixed crystals. It is found that the theoretical calculations presented in a previous paper agree generally with experiments except for cluster states observed in system (1) at lower guest concentrations. These features are discussed semi-quantitatively. As to the intermolecular interaction parameters, it is found that experimental results compare favorably with calculations based on experimental density-of-states functions but not with those based on octopole interactions or charge-transfer interactions. Previous experimental results of Sheka and the theoretical model of Broude and Rashba are also compared with present investigations.

PART III

The phosphorescence, fluorescence and absorption spectra of pyrazine-h₄ and d₄ have been obtained at 4˚K in a benzene matrix. For comparison, those of the isotopically mixed crystal pyrazine-h₄ in d₄ were also taken. All these spectra show extremely sharp and well-resolved lines and reveal detailed vibronic structure.

The analysis of the weak fluorescence spectrum resolves the long-disputed question of whether one or two transitions are involved in the near-ultraviolet absorption of pyrazine. The “mirror-image relationship” between absorption and emission shows that the lowest singlet state is an allowed transition, properly designated as ¹B_3u ← ¹A_1g. The forbidden component ¹B_2g, predicted by both “exciton” and MO theories to be below the allowed component, must lie higher. Its exact location still remains uncertain.

The phosphorescence spectrum when compared with the excitation phosphorescence spectra, indicates that the lowest triplet state is also symmetry allowed, showing a strong 0-0 band and a “mirror-image relationship” between absorption and emission. In accordance with previous work, the triplet state is designated as ³B_3u.

The vibronic structure of the phosphorescence spectrum is very complicated. Previous work on the analysis of this spectrum all concluded that a long progression of v_6a exists. Under the high resolution attainable in our work, the supposed v_6a progression proves to have a composite triplet structure, starting from the second member of the progression. Not only is the v_9a hydrogen-bending mode present as shown by the appearance of the C-D bending mode in the d₄ spectrum, but a band of 1207 cm^-1 in the pyrazine in benzene system and 1231 cm^-1 in the mixed crystal system is also observed. This band is assigned as 2v_6b and of a_1g symmetry. Its anonymously strong intensity in the phosphorescence spectrum is interpreted as due to the Fermi resonance with the 2v_6a and v_9a band.

To help resolve the present controversy over the crystal phosphorescence spectrum of pyrazine, detailed vibrational analyses of the emission spectra were made. The fluorescence spectrum has essentially the same vibronic structure as the phosphorescence spectrum.

Effects of annealing on the color, absorption spectra, and light yield of Ce : YAlO3 single crystal grown by the temperature gradient technique

YAlO3 single crystal doped with Ce3+ at concentration 1% was grown by the temperature gradient technique. The as-grown crystal was pink. After H-2 annealing or air annealing at 1400degreesC for 20 h, the crystal was turned into colorless. We concluded there were two kinds of color centers in the as-grown crystal. One is F+ center attributed to absorption band peaking at about 530 nm, the other is O- center attributed to absorption band peaking at about 390 nm. This color centers model can be applied in explaining the experiment phenomena including the color changes, the absorption spectra changes, and the light yield changes of Ce:YAP crystals before and after annealing. (C) 2004 American Institute of Physics.

Efficient laser oscillation of Yb : Y3Al5O12 single crystal grown by temperature gradient technique

Low-threshold and highly efficient continuous-wave laser performance of Yb:Y3Al5O12 (Yb:YAG) single crystal grown by a temperature gradient technique (TGT) was achieved at room temperature. The laser can be operated at 1030 and 1049 nm by varying the transmission of the output coupler. Slope efficiencies of 57% and 68% at 1049 and 1030 nm, respectively, were achieved for 10 at. % Yb:YAG sample in continuous-wave laser-diode pumping. The effect of pump power on the laser emission spectrum of both wavelengths is addressed. The near-diffraction-limited beam quality for different laser cavities was achieved. The excellent laser performance indicates that TGT-grown Yb:YAG crystals have very good optical quality and can be potentially used in high-power solid-state lasers.

Effects of gamma-irradiation and air annealing on Yb-doped Y3Al5O12 single crystal

The effects of gamma-irradiation on the air-annealed 10 at.% Yb:Y3Al5O12 (YAG) and air annealing on the gamma-irradiated 10at.% Yb:YAG have been studied by the difference absorption spectra before and after treatment. The gamma-irradiation and air annealing led to opposite changes of the absorption properties of the Yb:YAG crystal. After air annealing, the gamma-irradiation induced centers were totally removed and the concentration of Fe3+ and Yb3+ were lightly increased. For the first time, the gamma-irradiation induced valence changes between Yb3+ and Yb2+ ions in Yb:YAG crystals have been observed. (C) 2007 Elsevier B.V. All rights reserved.

Effect of size, morphology and crystallinity of seed crystal on the nucleation and growth of single grain Y-Ba-Cu-O

The effect of size, morphology and crystallinity of seed crystals on the nucleation and growth of large grain Y-Ba-Cu-O (YBCO) bulk superconductors fabricated by top seeded melt growth (TSMG) has been investigated. Seeding bulk samples with small, square shaped seed crystals leads to point nucleation and growth of the superconducting YBa2Cu3O7-y (Y-123) phase that exhibits the usual square habitual growth symmetry. The use of triangular and circular shaped seed crystals, however, modifies significantly the growth habit geometry of the grain. The use of large area seeds both increases the rate of epitaxial nucleation of the Y-123 phase and produces relatively large crystals in the incongruent melt, which decreases significantly the processing times of large grain samples. The present study is relevant to decrease processing times of samples with both preferred or no growth sectors and for multiple seeding of large grain samples which contain clean grain boundaries. © 2005 Published by Elsevier Ltd.

Photomechanically Induced Phase Transitions in Ferroelectric Liquid Crystals

We report optically induced phase transtions occurring in two different host ferroelectric liquid crystals; SCE13 a multicomponentmixture optimised for room temperature performance, and CE8 a single component liquid crystal. These act as host liquid crystals for a novel guest azo dye, which can be made to photoisomerise using low power density U.V. illumination, resulting in dramatic changes in sample properties. We have shown that the magnitude of spontaneous polarisation of systems can be isothermally and reversibly induced or reduced, with the consequent appearance or disappearance of optical switching hysteresis. We discuss the parameters controlling the behaviour of the systems under U.V. illumination and suggest mechansims by which the transitions may occur. © 1993, Taylor & Francis Group, LLC. All rights reserved.

A lattice dynamical treatment for the total potential energy of single-walled carbon nanotubes and its applications: relaxed equilibrium structure, elastic properties, and vibrational modes of ultra-narrow tubes

In this paper, we propose a lattice dynamic treatment for the total potential energy of single-walled carbon nanotubes (SWCNTs) which is, apart from a parameter for the nonlinear effects, extracted from the vibrational energy of the planar graphene sheet. The energetics, elasticity and lattice dynamics are treated in terms of the same set of force constants, independently of the tube structures. Based upon this proposal, we have investigated systematically the relaxed lattice configuration for narrow SWCNTs, the strain energy, the Young's modulus and Poisson ratio, and the lattice vibrational properties with respect to the relaxed equilibrium tubule structure. Our calculated results for various physical quantities are nicely in consistency with existing experimental measurements. In particular, we verified that the relaxation effect makes the bond length longer and the frequencies of various optical vibrational modes softer. Our calculation provides evidence that the Young's modulus of an armchair tube exceeds that of the planar graphene sheet, and that the large diameter limits of the Young's modulus and Poisson ratio are in agreement with the experimental values of graphite; the calculated radial breathing modes for ultra-narrow tubes with diameters ranging between 2 and 5 angstrom coincide with the experimental results and the existing ab initio calculations with satisfaction. For narrow tubes with a diameter of 20 angstrom, the calculated frequencies of optical modes in the tubule's tangential plane, as well as those of radial breathing modes, are also in good agreement with the experimental measurements. In addition, our calculation shows that various physical quantities of relaxed SWCNTs can actually be expanded in terms of the chiral angle defined for the corresponding ideal SWCNTs.

Space growth studies of Ce-doped Bi12SiO20 single crystal

Ce-doped Bi12SiO20 (BSO) single crystal was grown on board of the Chinese Spacecraft-Shenzhou No. 3. A cylindrical crystal, 10 mm in diameter and 40 mm in length, was obtained. The morphology of crystals is significantly different for ground- and space-grown portions. The space- and ground-grown crystals have been characterized by Cc concentration distribution, X-ray rocking curve absorption spectrum and micro-Raman spectrum. The results show that the quality of Ce-doped BSO crystal grown in space is more homogeneous and more perfect than that of ground grown one. (C) 2004 Published by Elsevier B.V.

Growth of CeO2 : Bi12SiO20 crystals in multi-position furnace(II) - Space growth experiment

Ce-doped Bi12SiO20 single crystal with size of phi10mm x 40mm was successfully grown in space on board of the spacecraft Shenzhou No.3. The surface morphology of space-grown crystal is different from that of ground-grown crystal The space- and ground-grown crystals were measured by X-ray rocking curves, absorption spectra and micro-Raman spectra. The results show that the quality of Ce-deped crystal grown in space is better than that of the ground-grown one. The effect of doping on optical properties of BSO grown in space is evident in comparison with the ground-grown crystal.

Effects and numerical analysis of argon gas flow on the oxygen concentration in Czochralski silicon single crystal growth

Argon gas, as a protective environment and carrier of latent heat, has an important effect on the temperature distribution in crystals and melts. Numeric simulation is a potent tool for solving engineering problems. In this paper, the relationship between argon gas flow and oxygen concentration in silicon crystals was studied systematically. A flowing stream of argon gas is described by numeric simulation for the first time. Therefore, the results of experiments can be explained, and the optimum argon flow with the lowest oxygen concentration can be achieved. (C) 2002 Elsevier Science B.V. All rights reserved.

Room temperature operation of photonic-crystal distributed-feedback quantum cascade lasers with single longitudinal and lateral mode performance

We demonstrate room temperature operation of photonic-crystal distributed-feedback quantum cascade lasers emitting at 4.7 mu m. A rectangular photonic crystal lattice perpendicular to the cleaved facet was defined using holographic lithography. The anticrossing of the index- and Bragg-guided dispersions of rectangular lattice forms the band-edge mode with extended mode volume and reduced group velocity. Utilizing this coupling mechanism, single mode operation with a near-diffractive-limited divergence angle of 12 degrees is obtained for 33 mu m wide devices in a temperature range of 85-300 K. The reduced threshold current densities and improved heat dissipation management contribute to the realization of devices' room temperature operation.

Color center conversion by femtosecond pulse laser irradiation in LiF : F-2 crystals

We report the observation of intense spontaneous emission of green light from LiF:F-2:F-3(+) centers in active channel waveguides generated in lithium fluoride crystals by near-infrared femtosecond laser radiation. While irradiating the crystal at room temperature with 405 nm light from a laser diode, yellow and green emission was seen by the naked eye. Stripe waveguides were fabricated by translating the crystal along the irradiated laser pulse, and their guiding properties and fluorescence spectra at 540 nm demonstrated. This single-step process inducing a waveguide structure offers a good prospect for the development of a waveguide laser in bulk LiF crystals.

Waveguides induced by screening-photovoltaic solitons in biased photorefractive-photovoltaic crystals

We investigate theoretically waveguides induced by screening-photovoltaic solitons in biased photorefractive-photovoltaic crystals. We show that the number of guided modes in a waveguide induced by a bright screening-photovoltaic soliton increases monotonically with the increasing intensity ratio of the soliton, which is the ratio between the peak intensity of the soliton and the dark irradiance. On the other hand, waveguides induced by dark screening-photovoltaic solitons are always single mode for all intensity ratios and the confined energy near the centre of a dark screening-photovoltaic soliton increases monotonically with the increasing intensity ratio. When the bulk photovoltaic effect is neglectable, these waveguides are those induced by screening solitons. When the external field is absent, these waveguides predict those induced by photovoltaic solitons.