The dispersive properties of an excited-doublet four-level atomic system

We have investigated the dispersive properties of excited-doublet four-level atoms interacting with a weak probe field and an intense coupling laser field. We have derived an analytical expression of the dispersion relation for a general excited-doublet four-level atomic system subject to a one-photon detuning. The numerical results demonstrate that for a typical rubidium D1 line configuration, due to the unequal dipole moments for the transitions of each ground state to double excited states, generally there exists no exact dark state in the system. Close to the two-photon resonance, the probe light can be absorbed orgained and propagate in the so-called superluminal form. This system may be used as an optical switch.

The design of a controllable imaging device with the cold atomic medium

Under the circumstance of a Gaussian control field, the cold atomic medium with electromagnetically induced transparency (EIT) turns out to be the special medium with the quadratic index distribution which is controllable online. In our study, the optical system occupies a portion of the EIT medium which acts as an imaging device. With the help of the Collins formula, the analytic expression for the spatial distribution of the probe field in the cold atomic medium is obtained as well as the location of the imaging. The methods for improving the visibility of the imaging are proposed in this paper. Moreover, we also show that the shapes of the images on the output are strongly influenced by the intensity of the control field, which provides a potential optical processing method.

Structure Prediction of G-Protein Coupled Receptors

G-protein coupled receptors (GPCRs) form a large family of proteins and are very important drug targets. They are membrane proteins, which makes computational prediction of their structure challenging. Homology modeling is further complicated by low sequence similarly of the GPCR superfamily.

In this dissertation, we analyze the conserved inter-helical contacts of recently solved crystal structures, and we develop a unified sequence-structural alignment of the GPCR superfamily. We use this method to align 817 human GPCRs, 399 of which are nonolfactory. This alignment can be used to generate high quality homology models for the 817 GPCRs.

To refine the provided GPCR homology models we developed the Trihelix sampling method. We use a multi-scale approach to simplify the problem by treating the transmembrane helices as rigid bodies. In contrast to Monte Carlo structure prediction methods, the Trihelix method does a complete local sampling using discretized coordinates for the transmembrane helices. We validate the method on existing structures and apply it to predict the structure of the lactate receptor, HCAR1. For this receptor, we also build extracellular loops by taking into account constraints from three disulfide bonds. Docking of lactate and 3,5-dihydroxybenzoic acid shows likely involvement of three Arg residues on different transmembrane helices in binding a single ligand molecule.

Protein structure prediction relies on accurate force fields. We next present an effort to improve the quality of charge assignment for large atomic models. In particular, we introduce the formalism of the polarizable charge equilibration scheme (PQEQ) and we describe its implementation in the molecular simulation package Lammps. PQEQ allows fast on the fly charge assignment even for reactive force fields.

Effect of Microstructural Interfaces on the Mechanical Response of Crystalline Metallic Materials

Advances in nano-scale mechanical testing have brought about progress in the understanding of physical phenomena in materials and a measure of control in the fabrication of novel materials. In contrast to bulk materials that display size-invariant mechanical properties, sub-micron metallic samples show a critical dependence on sample size. The strength of nano-scale single crystalline metals is well-described by a power-law function, σαD^-n, where D is a critical sample size and n is a experimentally-fit positive exponent. This relationship is attributed to source-driven plasticity and demonstrates a strengthening as the decreasing sample size begins to limit the size and number of dislocation sources. A full understanding of this size-dependence is complicated by the presence of microstructural features such as interfaces that can compete with the dominant dislocation-based deformation mechanisms. In this thesis, the effects of microstructural features such as grain boundaries and anisotropic crystallinity on nano-scale metals are investigated through uniaxial compression testing. We find that nano-sized Cu covered by a hard coating displays a Bauschinger effect and the emergence of this behavior can be explained through a simple dislocation-based analytic model. Al nano-pillars containing a single vertically-oriented coincident site lattice grain boundary are found to show similar deformation to single-crystalline nano-pillars with slip traces passing through the grain boundary. With increasing tilt angle of the grain boundary from the pillar axis, we observe a transition from dislocation-dominated deformation to grain boundary sliding. Crystallites are observed to shear along the grain boundary and molecular dynamics simulations reveal a mechanism of atomic migration that accommodates boundary sliding. We conclude with an analysis of the effects of inherent crystal anisotropy and alloying on the mechanical behavior of the Mg alloy, AZ31. Through comparison to pure Mg, we show that the size effect dominates the strength of samples below 10 μm, that differences in the size effect between hexagonal slip systems is due to the inherent crystal anisotropy, suggesting that the fundamental mechanism of the size effect in these slip systems is the same.

From molecules to organs : Microscopy and multi-scale nature of development

Morphogenesis is a phenomenon of intricate balance and dynamic interplay between processes occurring at a wide range of scales (spatial, temporal and energetic). During development, a variety of physical mechanisms are employed by tissues to simultaneously pattern, move, and differentiate based on information exchange between constituent cells, perhaps more than at any other time during an organism's life. To fully understand such events, a combined theoretical and experimental framework is required to assist in deciphering the correlations at both structural and functional levels at scales that include the intracellular and tissue levels as well as organs and organ systems. Microscopy, especially diffraction-limited light microscopy, has emerged as a central tool to capture the spatio-temporal context of life processes. Imaging has the unique advantage of watching biological events as they unfold over time at single-cell resolution in the intact animal. In this work I present a range of problems in morphogenesis, each unique in its requirements for novel quantitative imaging both in terms of the technique and analysis. Understanding the molecular basis for a developmental process involves investigating how genes and their products- mRNA and proteins-function in the context of a cell. Structural information holds the key to insights into mechanisms and imaging fixed specimens paves the first step towards deciphering gene function. The work presented in this thesis starts with the demonstration that the fluorescent signal from the challenging environment of whole-mount imaging, obtained by in situ hybridization chain reaction (HCR), scales linearly with the number of copies of target mRNA to provide quantitative sub-cellular mapping of mRNA expression within intact vertebrate embryos. The work then progresses to address aspects of imaging live embryonic development in a number of species. While processes such as avian cartilage growth require high spatial resolution and lower time resolution, dynamic events during zebrafish somitogenesis require higher time resolution to capture the protein localization as the somites mature. The requirements on imaging are even more stringent in case of the embryonic zebrafish heart that beats with a frequency of ~ 2-2.5 Hz, thereby requiring very fast imaging techniques based on two-photon light sheet microscope to capture its dynamics. In each of the hitherto-mentioned cases, ranging from the level of molecules to organs, an imaging framework is developed, both in terms of technique and analysis to allow quantitative assessment of the process in vivo. Overall the work presented in this thesis combines new quantitative tools with novel microscopy for the precise understanding of processes in embryonic development.

Optical intrinsically fuzzy mathematical morphology for gray-scale image processing

Intrinsically fuzzy morphological erosion and dilation are extended to a total of eight operations that have been formulated in terms of a single morphological operation--biased dilation. Based on the spatial coding of a fuzzy variable, a bidirectional projection concept is proposed. Thus, fuzzy logic operations, arithmetic operations, gray-scale dilation, and erosion for the extended intrinsically fuzzy morphological operations can be included in a unified algorithm with only biased dilation and fuzzy logic operations. To execute this image algebra approach we present a cellular two-layer processing architecture that consists of a biased dilation processor and a fuzzy logic processor. (C) 1996 Optical Society of America

Studies of the representation of interatomic distances in molecules and crystal as sum of atomic radii

The electron diffraction investigation of the following compounds has been carried out: sulfur, sulfur nitride, realgar, arsenic trisulfide, spiropentane, dimethyltrisulfide, cis and trans lewisite, methylal, and ethylene glycol.

The crystal structures of the following salts have been determined by x-ray diffraction: silver molybdateand hydrazinium dichloride.

Suggested revisions of the covalent radii for B, Si, P, Ge, As, Sn, Sb, and Pb have been made, and values for the covalent radii of Al, Ga, In, Ti, and Bi have been proposed.

The Schomaker-Stevenson revision of the additivity rule for single covalent bond distances has been used in conjunction with the revised radii. Agreement with experiment is in general better with the revised radii than with the former radii and additivity.

The principle of ionic bond character in addition to that present in a normal covalent bond has been applied to the observed structures of numerous molecules. It leads to a method of interpretation which is at least as consistent as the theory of multiple bond formation.

The revision of the additivity rule has been extended to double bonds. An encouraging beginning along these lines has been made, but additional experimental data are needed for clarification.

Morphological ordered gray-scale erosion for optical image processing

An ordered gray-scale erosion is suggested according to the definition of hit-miss transform. Instead of using three operations, two images, and two structuring elements, the developed operation requires only one operation and one structuring element, but with three gray-scale levels. Therefore, a union of the ordered gray-scale erosions with different structuring elements can constitute a simple image algebra to program any combined image processing function. An optical parallel ordered gray-scale erosion processor is developed based on the incoherent correlation in a single channel. Experimental results are also given for an edge detection and a pattern recognition. (C) 1998 Society of Photo-Optical Instrumentation Engineers. [S0091-3286(98)00306-7].

Optical multichannel-scale range-tunable Fourier-transforming system: experiment

The authors have demonstrated the principle of a novel optical multichannel-scale range-tunable Fourier-transforming system. The experimental results show good agreement with the theoretical analysis.