Multi-Band Optical Networks Capacity, Energy, and Techno-Economic Assessment

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The Packing Landscapes of Quasi-One Dimensional Hard Sphere Systems

When a liquid is cooled below its equilibrium freezing temperature, it becomes supercooled and the molecular motions slow down until the system becomes kinetically arrested, forming a glass, at the glass transition temperature. These amorphous materials have the mechanical properties of a solid while retaining the structural properties of a liquid, but do not exhibit the usual features of a thermodynamic phase transition. As such, they present a number of important challenges to our understanding of the dynamics and thermodynamics of condensed phases. For example, supercooled liquids are classified on the basis of the temperature dependence of their transport properties and structural relaxations times. Strong liquids display an Arrhenius behavior, with the logarithm of their viscosity growing linearly with inverse temperature. Fragile liquids behave in a super-Arrhenius manner, where the viscosity appears to diverge at temperatures above absolute zero, suggesting the possibility of an underlying thermodynamic origin to the glass transition. Some complex, network forming liquids, such as water and silica have also been shown to have a dynamical crossover from fragile to strong liquid behavior as the temperature is decreased. The potential energy landscape paradigm, combined with inherent structure formalism, provide a framework for connecting the way particles pack together with the thermodynamics and dynamics of the liquid and glassy phases. However, the complexity of this multi-dimensional surface makes it difficult to fully characterize and rigorous relationships between the nature of particle packing and glass forming properties have not been established. The goal of this thesis is to study some of the general features of glass transition and find the connection between the dynamics and the thermodynamics of glass forming liquids. To this end, the packing landscapes of quasi-one-dimensional hard discs and hard spheres are studied. A two dimensional system of hard discs with diameter σ, confined between two hard walls (lines) of length L, separated by a distance 1<Hd/σ< 1+√(3/4), is studied by using the Transfer Matrix (TM) method and Molecular Dynamics (MD) simulations. The complete packing landscape is characterized in terms of the density distribution of inherent structures and the number of local defect states. It is shown that this model exhibits a dynamic fragile-strong liquid crossover at the maximum in the constant pressure heat capacity (Cp) for the system, similar to that observed in anomalous network forming liquids such as water and silica. Furthermore, we find that rescaling the relaxation times of systems with different channel widths by the relaxation time at the Cp maximum causes all the data to collapse on a single master curve. The Cp maximum occurs at a critical value of the defect concentration. At high defect concentrations, where the defects interact, the fluid is fragile. When the defect concentration is low, relaxation appears to occur through the hopping of isolated defects, leading to Arrhenius dynamics. This suggests the thermodynamics associated with the Cp maximum is intimately related to the dynamic crossover. A system of three-dimensional hard spheres confined in a narrow channel was used to study the effect of a more complicated landscape on the dynamics of the system. For this system, the thermodynamic and dynamic properties of the system were studied for two different channel diameters, the 1<Hd/σ<1+√(3/4) case, which only allows first neighbors contact for the spheres and, 1+√(3/4)< Hd/σ < 1.98, which allows second neighbors contact to exist. For the first case, the TM method was implemented to obtain the thermodynamic properties and MD simulation was used to measure the dynamics. For the case that the second neighbor contact is allowed 1+√(3/4)< Hd/σ < 1.98. The thermodynamic and dynamic properties were obtained using MD simulations. In this channel diameter range, the system creates chiral helical jammed packings and defect states appear where sections of helices with different local chiralities come into contact. The equation of state (EOS) shows the presence of two heat capacity maxima. The high density Cp maximum is linked to fragile strong crossover. Finite size scaling analysis shows that the low density Cp maximum is related to an orientational order transition stabilized by the presence of the defects. This type of transition has been shown to exist in bulk two-dimensional systems but this work is the first study that provides strong evidence of the existence of this transition in a quasi-one-dimensional system in a system with short-range interactions

Molecular cloning and expression of novel fibroblast growth factor-2 conjugated with immunodominant domains of pseudomonas exotoxin

Angiogenesis is very important in cancer growth and metastasis. Basic fibroblast growth factor (bFGF) as one of the most important angiogenesis factors is an attractive target for cancer vaccine. Due to low immunogenicity, it cannot stimulate an effective immune response. Theoretically, pseudomonas exotoxin (PE) as a potent immunogenic carrier protein when fused to low immunogenic antigens such as bFGF significantly increased immunogenicity of it. In this study, we tried to molecular cloning and expression of bFGF conjugated with immunodominant domains of pseudomonas exotoxin. The coding sequence of fusion protein composed of bFGF linked to PE domains 1b and 2 using EAAAK poly linker. The KDEL sequence was also used in C-terminal coding sequence. It was synthesized and expressed using recombinant DNA technology in the bacterial expression system. Expression of recombinant protein verified using SDS-PAGE and western blot analyses. Finally, it purified using Ni-affinity chromatography. The band close to 37 kDa in SDS-PAGE and western blot analyses was aligned completely to designed sequence. Purified recombinant protein also showed as a clear single band near to 37 kDa

The Inherent Structure Landscape Connection Between Liquids, Granular materials and the Jamming Phase Diagram

We provide a comprehensive picture of the jamming phase diagram by connecting the athermal, granular ensemble of jammed states and the equilibrium fluid through the inherent structure paradigm for a system hard discs confined to a narrow channel. The J-line is shown to be divided into packings that are thermodynamically accessible from the equilibrium fluid and inaccessible packings. The J-point is found to occur at the transition between these two sets of packings and is located at the maximum the inherent structure distribution. A general thermodynamic argument suggests that the density of the states at the configurational entropy maximum represents a lower bound on the J-point density in hard sphere systems. Finally, we find that the granular and fluid systems only occupy the same set of inherent structures, under the same thermodynamic conditions, at two points, corresponding to zero and infinite pressures, where they sample the J-point states and the most dense packing respectively.Comment: 5 pages, 3 Figure

Limited Feedback Scheme for Device to Device Communications in 5G cellular networks with Reliability and Cellular Secrecy Outage Constraints

In this paper, we propose a device to device (D2D) communication scenario underlaying a cellular network where both D2D and cellular users (CUs) are discrete power-rate systems with limited feedback from the receivers. It is assumed that there exists an adversary which wants to eavesdrop on the information transmission from the base station (BS) to CUs. Since D2D communication shares the same spectrum with cellular network, cross interference must be considered. However, when secrecy capacity is considered, the interference caused by D2D communication can help to improve the secrecy communications by confusing the eavesdroppers. Since both systems share the same spectrum, cross interference must be considered. We formulate the proposed resource allocation into an optimization problem whose objective is to maximize the average transmission rate of D2D pair in the presence of the cellular communications under average transmission power constraint. For the cellular network, we require a minimum average achievable secrecy rate in the absence of D2D communication as well as a maximum secrecy outage probability in the presence of D2D communication which should be satisfied. Due to high complexity convex optimization methods, to solve the proposed optimization problem, we apply Particle Swarm Optimization (PSO) which is an evolutionary approach. Moreover, we model and study the error in the feedback channel and the imperfectness of channel distribution information (CDI) using parametric and nonparametric methods. Finally, the impact of different system parameters on the performance of the proposed scheme is investigated through simulations. The performance of the proposed scheme is evaluated using numerical results for different scenarios.Comment: IEEE Transactions on Vehicular Technology, 201

Molecular dynamic simulation of Ca2+‐ATPase interacting with lipid bilayer membrane

In biomedical and drug delivery treatments, protein Ca2+-ATPase in the lipid bilayer ( plasma) membrane plays a key role by reducing multidrug resistance of the cancerous cells. The lipid bilayer membrane and the protein Ca2+-ATPase were simulated by utilising the Gromacs software and by applying the all-atom/united atom and coarse-grained models. The initial structure of Ca2+-ATPase was derived from X-ray diffraction and electron microscopy patterns and was placed in a simulated bilayer membrane of dipalmitoylphosphatidylcholine. The conformational changes were investigated by evaluating the root mean square deviation, root mean square fluctuation, order parameter, diffusion coefficients, partial density, thickness and area per lipid