I. The 3.7 Å crystal structure of horse heart ferricytochrome C. II. The application of the Karle-Hauptman tangent formula to protein phasing

I. The 3.7 Å Crystal Structure of Horse Heart Ferricytochrome C.

The crystal structure of horse heart ferricytochrome c has been determined to a resolution of 3.7 Å using the multiple isomorphous replacement technique. Two isomorphous derivatives were used in the analysis, leading to a map with a mean figure of merit of 0.458. The quality of the resulting map was extremely high, even though the derivative data did not appear to be of high quality.

Although it was impossible to fit the known amino acid sequence to the calculated structure in an unambiguous way, many important features of the molecule could still be determined from the 3.7 Å electron density map. Among these was the fact that cytochrome c contains little or no α-helix. The polypeptide chain appears to be wound about the heme group in such a way as to form a loosely packed hydrophobic core in the molecule.

The heme group is located in a cleft on the molecule with one edge exposed to the solvent. The fifth coordinating ligand is His 18 and the sixth coordinating ligand is probably neither His 26 nor His 33.

The high resolution analysis of cytochrome c is now in progress and should be completed within the next year.

II. The Application of the Karle-Hauptman Tangent Formula to Protein Phasing.

The Karle-Hauptman tangent formula has been shown to be applicable to the refinement of previously determined protein phases. Tests were made with both the cytochrome c data from Part I and a theoretical structure based on the myoglobin molecule. The refinement process was found to be highly dependent upon the manner in which the tangent formula was applied. Iterative procedures did not work well, at least at low resolution.

The tangent formula worked very well in selecting the true phase from the two possible phase choices resulting from a single isomorphous replacement phase analysis. The only restriction on this application is that the heavy atoms form a non-centric cluster in the unit cell.

Pages 156 through 284 in this Thesis consist of previously published papers relating to the above two sections. References to these papers can be found on page 155.

Isolation and characteristics of a bacteriophage for bacillus stearothermophilus

A bacteriophage (TØ3) which infects the thermophilic bacterium Bacillus stearothermophilus ATCC 8005 was isolated and characterized. Infection of the bacterium by the bacteriophage was carried out at 60°C, the optimum growth temperature of the host. At 60°C the phage has a latent period of 18 minutes and a burst size of about 200. The phage is comparatively thermostable in broth. The half life of the phage is 400 minutes at 60°C, 120 minutes at 65°C, 40 minutes at 70°C and 12 minutes at 75°C. The activation energy for the heat inactivation of TØ3 is 56,000 cal. The buoyant density of TØ3 in a cesium chloride density gradient is 1.526.

Electron micrographs of TØ3 indicate that the phage has a regular hexagonal shaped head 57 mμ long. The morphology of the head is compatible with icosahedral symmetry. Each edge of the head is 29 mμ long, and there are 6 or 7 subunits along each edge. The tail of TØ3 is 125 mμ long and 10 mμ wide. There are about 30 cross striations that are spaced at 3.9 mμ intervals along the tail.

The DNA of phage TØ3 has a melting temperature of 88.5°C. Heat denatured TØ3 DNA can be extensively annealed in a high ionic strength environment. The buoyant density of TØ3 DNA in a cesium chloride density gradient is 1.695. TØ3 DNA contains: 42.7% guanine plus cytosine, as determined from the melting temperature; 43% guanine plus cytosine, as determined from the buoyant density; and 40.2% guanine plus cytosine, as determined by chromatographic separation and spectrophotometric estimation of the bases. The molecular weight of TØ3 DNA is 16.7 X 10⁶ as determined from the band width of the TØ3 DNA concentration distribution in a cesium chloride density gradient. Electron microscopy of TØ3 DNA revealed a single linear molecule that is 11.7 μ long. This corresponds to a molecular weight of 22.5 X 10⁶.

Heat denatured TØ3 DNA forms two bands in a cesium chloride density gradient, one at a density of 1.707 and the other at a density of 1.715. After the separated bands are mixed and annealed in the centrifuge cell, the renatured TØ3 DNA forms a single band at a density of 1.699. These results indicate that the two complementary strands of TØ3 DNA have different buoyant densities in cesium chloride, presumably because they have different base compositions.

The characteristics of TØ3 are compared with those of other phages. A hypothesis is presented for a relationship between the base composition of one strand of TØ3 DNA and the amino acid composition of the proteins of TØ3.

Computational Microscopy: Breaking the Limit of Conventional Optics

Computational imaging is flourishing thanks to the recent advancement in array photodetectors and image processing algorithms. This thesis presents Fourier ptychography, which is a computational imaging technique implemented in microscopy to break the limit of conventional optics. With the implementation of Fourier ptychography, the resolution of the imaging system can surpass the diffraction limit of the objective lens's numerical aperture; the quantitative phase information of a sample can be reconstructed from intensity-only measurements; and the aberration of a microscope system can be characterized and computationally corrected. This computational microscopy technique enhances the performance of conventional optical systems and expands the scope of their applications.

Read-only memory disk with AgOx super-resolution mask layer

A novel read-only memory (ROM) disk with an AgOx mask layer was proposed and studied in this letter. The AgOx films sputtered on the premastered substrates, with pits depth of 50 nm and pits length of 380 nm, were studied by an atomic force microscopy. The transmittances of these AgOx films were also measured by a spectrophotometer. Disk measurement was carried out by a dynamic setup with a laser wavelength of 632.8 nm and a lens numerical aperture (NA) of 0.40. The readout resolution limit of this setup was λ/(4NA) (400 nm). Results showed that the super-resolution readout happened only when the oxygen flow ratios were at suitable values for these disks. The best super-resolution performance was achieved at the oxygen flow ratio of 0.5 with the smoothest film surface. The super-resolution readout mechanism of these ROM disks was analyzed as well.

Crystallization of amorphous Ge2Sb2Te5 films induced by a single femtosecond laser pulse

Crystallization is achieved in amorphous Ge2Sb2Te5 films upon irradiation with a single femtosecond laser pulse. Transmission electron microscopy images evidence the morphology of the crystallized spot which depends on the fluence of the ferntosecond laser pulse. Fine crystalline grains are induced at low fluence, and the coarse crystalline grains are obtained at high fluence. At the damage fluence, ablation of the films occurs. (C) 2004 Elsevier Ltd. All rights reserved.

Femtosecond laser pulse irradiation of Sb-rich AgInSbTe films: Scanning electron microscopy and atomic force microscopy investigations

The single-layer and multilayer Sb-rich AgInSbTe films were irradiated by a single femtosecond laser pulse with the duration of 120 fs. The morphological feature resulting from the laser irradiation have been investigated by scanning electron microscopy and atom force microscopy. For the single-layer film, the center of the irradiated spot is a dark depression and the border is a bright protrusion; however, for the multilayer film, the center morphology changes from a depression to a protrusion as the energy increases. The crystallization threshold fluence of the single-layer and the multilayer films is 46.36 mJ/cm(2), 63.74 mJ/cm(2), respectively.

Morphological characteristics of amorphous Ge2Sb2Te5 films after a single femtosecond laser pulse irradiation

The morphology of materials resulting from laser irradiation of the single-layer and the multilayer amorphous Ge2Sb2Te5 films using 120 fs pulses at 800 nm was observed using scanning electron microscopy and atomic force microscopy. For the single-layer film, the center of the irradiated spot is depression and the border is protrusion, however, for the multilayer film, the center morphology changes from a depression to a protrusion as the increase of the energy. The crystallization threshold fluence of the single-layer and the multilayer film is 22 and 23 mJ/cm(2), respectively. (c) 2005 Elsevier B.V. All rights reserved.

Super-resolution with a nonlinear thin film: Beam reshaping via internal multi-interference

In laser applications, the size of the focus spot can be reduced beyond the diffraction limit with a thin film of strong nonlinear optical Kerr effect. We present a concise theoretical simulation of the device. The origin of the super-resolution is found to be mainly from the reshaping effect due to the strongly nonlinear refraction mediated multi-interference inside the thin film. In addition, both diffraction and self-focusing effects have been explored and found negligible for highly refractive and ultrathin films in comparison with the reshaping effect. Finally, the theoretic model has been verified in experiments with single Ge2Sb2Te5 film and SiN/Si/SiN/Ge2Sb2Te2 multilayer structures. (c) 2006 American Institute of Physics.

Investigation on the static recording characteristic of super-resolution near-field structure with antimony mask layer

Static recording characteristic of super-resolution near-field structure with antimony (Sb) is investigated in this paper. The recording marks are observed by a scanning electron microscopy (SEM), a high-resolution optical microscopy with a CCD camera and an atomic force microscopy (AFM). The super-resolution mechanism is also analyzed based on these static recording marks. Results show that the light reaching on recording layer is composed of two parts, one is the linear transmissive light (propagating field) and the other is the nonlinear evanescent light in the optical near field. The evanescent light may be greatly enhanced in the center of the spot because Sb will transit from a semiconductor to a metal when it is melted under the high laser power irradiation. This local melted area in the spot center may be like a metal tip in the optical near field that can collect and enhance the information that is far beyond the diffraction limit, which leads to the super-resolution recording and readout. (c) 2005 Elsevier Ltd. All rights reserved.

ScAlMgO_4晶体的生长缺陷

采用提拉法生长出φ30 mm×55 mm的ScAlMgO4晶体。在晶体生长过程中有轻微的挥发,粉末X射线衍射分析表明:挥发物质为MgO单相。运用扫描电镜、光学显微镜以及高分辨X射线衍射仪对晶体中的包裹物、开裂、生长条纹和小角晶界缺陷进行了研究。结果表明:温度梯度和热应力是形成晶体中缺陷的主要原因。通过合理设计温场,控制固-液界面的形状及冷却过程的降温速率,可以提高晶体的完整性。

Growth and characterization of high-quality LiAlO2 single crystal

g-LiAlO2 single crystal is a promising substrate for GaN heteroepitaxy. In this paper, we present the growth of large-sized LiAlO2 crystal by modified Czochralski method. The crystal quality was characterized by high-resolution X-ray diffraction and chemical etching. The results show that the as-grown crystal has perfect quality with the full width at half maximum (FWHM) of 17.7-22.6 arcsec and etch pits density of (0.3-2.2) x 10(4) cm(-2) throughout the crystal boule. The bottom of the crystal boule shows the best quality. The optical transmission spectra from UV to IR exhibits that the crystal is transparent from 0.2 to 5.5 mu m and becomes completely absorbing around 6.7 mu m wavelength. The optical absorption edge in near UV region is about 191 nm.

离子束溅射法薄膜生长中结瘤微缺陷的生长机理

用离子束溅射法制备了锆单层薄膜．用设计新型夹具和预置种子方法，对薄膜中结瘤微缺陷的生长过程进行了研究．在高分辨率光学显微镜和扫描电子显微镜下观察发现，结瘤在其生长初期呈现出分形的特征．用分子动力学和薄膜生长的扩散限制聚集模型，薄膜中结瘤微缺陷成核时的分形现象得到了很好的解释．

Spectral measurement of diode lasers with a single-mode birefringent fibre

A new, and very simple spectrometer based on birefringent fiber is described. A resolution of 0.02 angstrom has been achieved, and the system has been used to measure diode laser chirp. A length of 10km of fiber would be sufficient to resolve single mode line widths.

mtDNA Data Indicate a Single Origin for Dogs South of Yangtze River, Less Than 16,300 Years Ago, from Numerous Wolves

There is no generally accepted picture of where, when, and how the domestic dog originated. Previous studies of mitochondrial DNA (mtDNA) have failed to establish the time and precise place of origin because of lack of phylogenetic resolution in the so fa

A single amino acid defines cross-species reactivity of tree shrew (Tupaia belangeri) CD1d to human invariant natural killer T (iNKT) cells

P>The non-classical major histocompatibility complex (MHC) class I molecule CD1d presents lipid antigens to invariant natural killer T (iNKT) cells, which are an important part of the innate immune system. CD1d/iNKT systems are highly conserved in evoluti