Generating artificial homologous proteins according to the representative family character in molecular mechanics properties - an attempt in validating an underlying rule of protein evolution

The molecular mechanics property is the foundation of many characters of proteins. Based on intramolecular hydrophobic force network, the representative family character underlying a protein’s mechanics property is described by a simple two-letter scheme. The tendency of a sequence to become a member of a protein family is scored according to this mathematical representation. Remote homologs of the WW-domain family could be easily designed using such a mechanistic signature of protein homology. Experimental validation showed that nearly all artificial homologs have the representative folding and bioactivity of their assigned family. Since the molecular mechanics property is the only consideration in this study, the results indicate its possible role in the generation of new members of a protein family during evolution.

A model for energy and morphology of crystalline grain boundaries with arbitrary geometric character

It has been well-established that interfaces in crystalline materials are key players in the mechanics of a variety of mesoscopic processes such as solidification, recrystallization, grain boundary migration, and severe plastic deformation. In particular, interfaces with complex morphologies have been observed to play a crucial role in many micromechanical phenomena such as grain boundary migration, stability, and twinning. Interfaces are a unique type of material defect in that they demonstrate a breadth of behavior and characteristics eluding simplified descriptions. Indeed, modeling the complex and diverse behavior of interfaces is still an active area of research, and to the author's knowledge there are as yet no predictive models for the energy and morphology of interfaces with arbitrary character. The aim of this thesis is to develop a novel model for interface energy and morphology that i) provides accurate results (especially regarding "energy cusp" locations) for interfaces with arbitrary character, ii) depends on a small set of material parameters, and iii) is fast enough to incorporate into large scale simulations.

In the first half of the work, a model for planar, immiscible grain boundary is formulated. By building on the assumption that anisotropic grain boundary energetics are dominated by geometry and crystallography, a construction on lattice density functions (referred to as "covariance") is introduced that provides a geometric measure of the order of an interface. Covariance forms the basis for a fully general model of the energy of a planar interface, and it is demonstrated by comparison with a wide selection of molecular dynamics energy data for FCC and BCC tilt and twist boundaries that the model accurately reproduces the energy landscape using only three material parameters. It is observed that the planar constraint on the model is, in some cases, over-restrictive; this motivates an extension of the model.

In the second half of the work, the theory of faceting in interfaces is developed and applied to the planar interface model for grain boundaries. Building on previous work in mathematics and materials science, an algorithm is formulated that returns the minimal possible energy attainable by relaxation and the corresponding relaxed morphology for a given planar energy model. It is shown that the relaxation significantly improves the energy results of the planar covariance model for FCC and BCC tilt and twist boundaries. The ability of the model to accurately predict faceting patterns is demonstrated by comparison to molecular dynamics energy data and experimental morphological observation for asymmetric tilt grain boundaries. It is also demonstrated that by varying the temperature in the planar covariance model, it is possible to reproduce a priori the experimentally observed effects of temperature on facet formation.

Finally, the range and scope of the covariance and relaxation models, having been demonstrated by means of extensive MD and experimental comparison, future applications and implementations of the model are explored.

On the character of the phytoplankton of the Yakimvarskii Gulf (Lake Ladoga) [Translation from: Botanicheskii Zhurnal, T. 44, No. 9, 1311-1314, 1959]

The Laboratory of Lake Studies of the Academy of Sciences of the USSR in 1956 undertook this complicated study of Lake Ladoga. The plan of the laboratory made allowance for the detailed investigation of the phytoplankton of the lake during a series of years. In the present article are given the preliminary results of observations on the phytoplankton of the Yakimvarskii Bay from 1956 to 1957. Details are also given on the concentration of dissolved gases and biogenic substances of the bay.

Syllable language models for Mandarin speech recognition: exploiting character language models.

Mandarin Chinese is based on characters which are syllabic in nature and morphological in meaning. All spoken languages have syllabiotactic rules which govern the construction of syllables and their allowed sequences. These constraints are not as restrictive as those learned from word sequences, but they can provide additional useful linguistic information. Hence, it is possible to improve speech recognition performance by appropriately combining these two types of constraints. For the Chinese language considered in this paper, character level language models (LMs) can be used as a first level approximation to allowed syllable sequences. To test this idea, word and character level n-gram LMs were trained on 2.8 billion words (equivalent to 4.3 billion characters) of texts from a wide collection of text sources. Both hypothesis and model based combination techniques were investigated to combine word and character level LMs. Significant character error rate reductions up to 7.3% relative were obtained on a state-of-the-art Mandarin Chinese broadcast audio recognition task using an adapted history dependent multi-level LM that performs a log-linearly combination of character and word level LMs. This supports the hypothesis that character or syllable sequence models are useful for improving Mandarin speech recognition performance.

Phylogenetic relationships of the Chinese cyprinid genus Rhinogobio Bleeker (Teleostei : Cyprinidae) based on sequences of the mitochondrial DNA control region, with comments on character adaptations

Rhinogobio is a cyprinid genus restricted to the river drainages of China. Sequences of the mitochondrial DNA control region were determined for four Rhinogohio species and one outgroup species, Coreius heterodon, to investigate the phylogenetic relationships within the genus. The control region of the Rhinogobio species ranges from 922 to 930 base pairs and comprises 930 base pairs in Coreius. Our phylogenetic analysis indicates two distinct lineages in the genus Rhinogobio. The first includes only R. ventralis. In the second lineage there are three species, two closely related species R. cylindricus and R. hunanensis, and their sister species R. typus. An analysis of character adaptations suggests an evolutionary trend in this genus towards a relatively lower body and caudal peduncle depth, a shorter dorsal fin, and a more anterior anus. In addition, there is a trend towards shorter barbels and relatively larger eyes. Some or all of these traits may be associated with a habitat shift from fast-flowing turbid rivers to slower-flowing clear river habitats.

The structural and photoluminescence character of InAs quantum dots grown on a combined InAlAs and GaAs strained buffer

The structural and photoluminescence (PL) properties of the InAs quantum dots (QDs) grown on a combined InAlAs and GaAs strained buffer layer have been investigated by AFM and PL measurements. The dependence of the critical thickness for the transition from 2D to 3D on the thickness of GaAs layer is demonstrated directly by RHEED. The effects of the introduced-InAlAs layer on the density and the aspect ratio of QDs have been discussed.

Phase character of the electron transport through a double quantum dot in a mesoscopic ring

We theoretically study the electron transport through a double quantum dot (QD) in the Coulomb blockade regime and reveal the phase character of the transport by embedding the double QD in a mesoscopic Aharonov-Bohm ring. It is shown that coherent transport through the double QD is preserved in spite of intradot and interdot Coulomb interactions.

Photoluminescence character of Xe ion irradiated sapphire

In the present work the photoluminescence (PL) character of sapphire implanted with 180 keV Xe and irradiated with 308 MeV Xe ions was studied. The virgin, implanted and irradiated samples were investigated by PL and Fourier transform infrared (FTIR) spectra measurements. The obtained PL spectra showed the maximum emission bands at 2.75, 3.0 and 3.26 eV for the implanted fluence of 1.0 x 10(15) ions/cm(2) and at 2.4 and 3.47 eV for the irradiated fluence of 1.0 x 10(13) ions/cm(2). The FTIR spectra showed a broaden absorption band between 460 and 630 cm(-1), indicating that strong damaged region formed in Al2O3.