Sharif Digital Repository

The number of known proteins is increasing every day; tens of thousands have been studied and categorized by now. In this chapter, we propose amodel for protein matching or extracting similar parts of two given proteins. We focus on the computational geometric approach and the graph matching method that are used to model and compare the sequence and 3D structure of proteins. The remainder ofthis chapter is organized as follows. We first have a glance at the related works. There are two major methods used in the literature: Delaunay tetrahedralization and similarity flooding.We explain the required information in the next section as background knowledge, and then propose a new idea in Sect.... 

Proteins are the main players in the game of life. Good understanding of their structures, functions, and behaviors leads to good understanding of drugs, diseases, and thus our health. So, much effort has been done to study and categorize proteins. Nowadays, tens of thousands of proteins have been found. Moreover, the problem of comparing the proteins is hard. Therefore efficient methods are needed to deal with this problem. In this paper, we used one important computational geometric method and one graph matching method: "Delaunay Tetrahedral-ization" and "Similarity Flooding" to propose a new idea to extract similar parts of proteins by combining both of these methods  

Nematic shells of liquid crystals have been provided in microscales. Defect structures in the shells are very essential in the electro-optical applications of such colloidal objects. We have numerically minimized the free energy of symmetric and asymmetric spherical shells of the nematic liquid crystal. Considering degenerate planar anchoring on the surfaces and isotropic nematic elasticity, a variety of defect structures are observed by controlling or varying the thicknesses of the shell and its degree of asymmetry. In symmetric shells, our calculations show that boojums (bipolar) defects appear in thick shells and tetrahedral (baseball) defects in thin shells. In asymmetric shells, while... 

M-type Ce–Co substituted barium hexaferrite nanoparticles were synthesized by sol–gel auto-combustion route. The general formula of ferrites was Ba1−xCexFe12−xCoxO19 in which the x was considered to be: x = 0, 0.1, 0.2, and 0.3. The formed phases in the samples were characterized by using X-ray diffraction, Fourier transform infrared spectroscopy, Mössbauer spectroscopy and vibrating sample magnetometer. The results indicated that an increase in substitutional ion amount caused to decrease vibration frequencies of Fe–O band in the tetrahedral site due to the substitution of heavier Co2+ ion for Fe3+ ion in the tetrahedral site. Moreover, some of Ce3+ ions was transformed to Ce4+ and... 

In this paper, the three-dimensional automatic adaptive mesh refinement is presented in modeling the crack propagation based on the modified superconvergent patch recovery technique. The technique is developed for the mixed mode fracture analysis of different fracture specimens. The stress intensity factors are calculated at the crack tip region and the crack propagation is determined by applying a proper crack growth criterion. An automatic adaptive mesh refinement is employed on the basis of modified superconvergent patch recovery (MSPR) technique to simulate the crack growth by applying the asymptotic crack tip solution and using the collapsed quarter-point singular tetrahedral elements... 

Ferrite nanocrystals are an interesting material due to their rich physical properties. Here we add nonmagnetic dopants Zn and Cu to nickel ferrite nanocrystals, Ni1-xMxFe2O4 (0 ≤ x ≤ 1, M = Cu, Zn), and study how relevant properties of the samples are modified accordingly. Basically, these dopings cause a rearrangement of Fe +3 ions into the two preexisting octahedral and tetrahedral sites. In fact, this, we show, induces pertinent magnetic properties of the doped samples. In the case of the Cu-doping, the Jahn-Teller effect also emerges, which we identify through the Fourier Transform Infra-Red Spectroscopy of the samples. Moreover, we show an increase in the lattice parameters of the... 

First principles density functional theory (DFT)-based molecular dynamics (MD) is used to study some physical and electronic properties of amorphous silicon (a-Si) samples, as-quenched and annealed containing dangling and floating bonds (pertinent to the threefold- and fivefold-coordinated defects, respectively) as well as distorted tetrahedral bonds. Surprisingly, except for the work of Pantelides (1986) who gave a rough estimate for the effective electron correlation energy, Ueff of a floating bond on the fivefold-coordinated Si, to date, there are no theoretical studies in the literature for the calculation of Ueff pertinent to this type of defect. In this work, Ueff for each type of... 

Depending on the type of dopant metal, many kinds of zircon based pigments are produced and blue vanadium pigment is the most important one of them. In this study, blue zircon ceramic pigments were synthesized from intermediate product, resulting from decomposition of zircon sand with NaOH. In this regard, various amounts of sulfuric acid, water, NH4VO3 as colorant, NaF as mineralizer and extra quartz were added to the prepared Na 2ZrSiO5. Role of quartz was to omit the repercussions of presence of free zirconia in the composition. The main objective of this work is to assess various reactions at different temperatures during blue pigment synthesis. Phase analysis was done by X ray... 

We study the quantum plasmonic features of gold and silver nanoparticles using TD-DFT+TB, a new density functional theory approach to the calculation of excited states, which combines a full DFT ground state with tight-binding approximations in the linear response calculation. In this framework, the optical properties of closed-shell Ag, Au and bimetallic Ag-Au nanoparticles with tetrahedral symmetry (with 20, 56, 120, and 165 atoms) and icosahedral structure (with 13, 55, and 147 atoms) were obtained and compared to full linear response time-dependent density functional theory (TD-DFT) as a reference and also to time-dependent density functional based tight binding (TD-DFTB) as a low-cost...